details: http://www.bx.psu.edu/hg/galaxy/rev/cc8a30a0669f changeset: 3570:cc8a30a0669f user: fubar: ross Lazarus at gmail period com date: Fri Mar 26 14:42:15 2010 -0400 description: Adding rg test outputs and updated tools diffstat: .hgignore | 4 + test-data/rgCaCotest1_CaCo.xls | 26 + test-data/rgCaCotest1_CaCo_log.txt | 46 + test-data/rgCaCotest1_CaCo_topTable.gff | 26 + test-data/rgGLM_GLM_topTable.gff | 26 + test-data/rgGLMtest1_GLM.xls | 26 + test-data/rgGLMtest1_GLM_log.txt | 58 + test-data/rgQQtest1.pdf | 384 ++ test-data/rgTDTtest1_TDT.xls | 25 + test-data/rgTDTtest1_TDT_log.txt | 53 + test-data/rgTDTtest1_TDT_topTable.gff | 25 + test-data/rgtestouts/rgClean/rgCleantest1.bed | 1 + test-data/rgtestouts/rgClean/rgCleantest1.bim | 25 + test-data/rgtestouts/rgClean/rgCleantest1.fam | 40 + test-data/rgtestouts/rgClean/rgCleantest1.log | 66 + test-data/rgtestouts/rgClean/rgCleantest1.pbed | 19 + test-data/rgtestouts/rgEigPCA/Rplots.pdf | 59 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R | 19 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html | 160 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt | 40 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf | 454 +++ test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf.png | 0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf | 0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps | 502 +++ test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt | 7 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls | 39 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt | 128 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls | 45 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec | 40 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par | 11 + test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 23 + test-data/rgtestouts/rgGRR/rgGRRtest1.html | 65 + test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 770 +++++ test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 781 +++++ test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf | 0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png | 0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG | 0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt | 50 + test-data/rgtestouts/rgHaploView/alljoin.pdf | 0 test-data/rgtestouts/rgHaploView/allnup.pdf | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html | 124 + test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS | 25 + test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS | 9 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed | 1 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim | 3 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam | 40 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log | 169 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map | 3 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.pbed | 22 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped | 40 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in | 3 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out | 22 + test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 150 + test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 61 + test-data/rgtestouts/rgPedSub/rgPedSubtest1.log | 12 + test-data/rgtestouts/rgPedSub/rgPedSubtest1.lped | 17 + test-data/rgtestouts/rgPedSub/tinywga.map | 10 + test-data/rgtestouts/rgPedSub/tinywga.ped | 40 + test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 373 ++ test-data/rgtestouts/rgQC/MarkerDetails_rgQCtest1.xls | 1 + test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls | 21 + test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls | 41 + test-data/rgtestouts/rgQC/ldp_tinywga.bed | 1 + test-data/rgtestouts/rgQC/ldp_tinywga.bim | 14 + test-data/rgtestouts/rgQC/ldp_tinywga.fam | 40 + test-data/rgtestouts/rgQC/ldp_tinywga.log | 48 + test-data/rgtestouts/rgQC/rgQCtest1.html | 576 ++++ test-data/rgtestouts/rgQC/tinywga.fmendel | 14 + test-data/rgtestouts/rgQC/tinywga.frq | 26 + test-data/rgtestouts/rgQC/tinywga.het | 41 + test-data/rgtestouts/rgQC/tinywga.hwe | 76 + test-data/rgtestouts/rgQC/tinywga.imendel | 40 + test-data/rgtestouts/rgQC/tinywga.imiss | 41 + test-data/rgtestouts/rgQC/tinywga.lmendel | 26 + test-data/rgtestouts/rgQC/tinywga.lmiss | 26 + test-data/rgtestouts/rgQC/tinywga.log | 48 + test-data/rgtestouts/rgQC/tinywga.mendel | 1 + test-data/rgtestouts/rgQC/tinywga.prune.in | 14 + test-data/rgtestouts/rgQC/tinywga.prune.out | 11 + test-data/rgtestouts/rgQC/tinywga.sexcheck | 41 + test-data/rgtestouts/rgQC/tinywga_All_3x3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf | 333 ++ test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 369 ++ test-data/rgtestouts/rgQC/tinywga_s_het.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 344 ++ test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 379 ++ test-data/rgtestouts/rgfakePed/rgfakePedtest1.lped | 16 + test-data/rgtestouts/rgfakePed/rgfakePedtest1.map | 10 + test-data/rgtestouts/rgfakePed/rgfakePedtest1.ped | 40 + test-data/rgtestouts/rgfakePhe/rgfakePhetest1.pphe | 41 + test-data/rgtestouts/rgfakePhe/script_file | 7 + tools/rgenetics/listFiles.py | 227 + tools/rgenetics/plinkbinJZ.py | 868 ++++++ tools/rgenetics/rgCaCo.py | 282 ++ tools/rgenetics/rgCaCo.xml | 101 + tools/rgenetics/rgCaCo_code.py | 45 + tools/rgenetics/rgClean.py | 160 + tools/rgenetics/rgClean.xml | 155 + tools/rgenetics/rgClean_code.py | 28 + tools/rgenetics/rgEigPCA.py | 385 ++ tools/rgenetics/rgEigPCA.xml | 142 + tools/rgenetics/rgEigPCA_code.py | 27 + tools/rgenetics/rgGLM.py | 286 ++ tools/rgenetics/rgGLM.xml | 139 + tools/rgenetics/rgGLM_code.py | 59 + tools/rgenetics/rgGRR.py | 1092 ++++++++ tools/rgenetics/rgGRR.xml | 94 + tools/rgenetics/rgGRR_code.py | 23 + tools/rgenetics/rgGTOOL.py | 58 + tools/rgenetics/rgGTOOL.xml | 54 + tools/rgenetics/rgGTOOL_code.py | 19 + tools/rgenetics/rgHaploView.py | 521 +++ tools/rgenetics/rgHaploView.xml | 153 + tools/rgenetics/rgHaploView_code.py | 84 + tools/rgenetics/rgLDIndep.py | 182 + tools/rgenetics/rgLDIndep.xml | 157 + tools/rgenetics/rgLDIndep_code.py | 25 + tools/rgenetics/rgManQQ.py | 223 + tools/rgenetics/rgManQQ.xml | 117 + tools/rgenetics/rgManQQ_code.py | 50 + tools/rgenetics/rgPedSub.py | 305 ++ tools/rgenetics/rgPedSub.xml | 143 + tools/rgenetics/rgPedSub_code.py | 78 + tools/rgenetics/rgQC.py | 1334 ++++++++++ tools/rgenetics/rgQC.xml | 109 + tools/rgenetics/rgQC_code.py | 38 + tools/rgenetics/rgQQ.py | 365 ++ tools/rgenetics/rgQQ.xml | 99 + tools/rgenetics/rgQQ_code.py | 72 + tools/rgenetics/rgRegion.py | 80 + tools/rgenetics/rgRegion.xml | 60 + tools/rgenetics/rgRegion_code.py | 47 + tools/rgenetics/rgTDT.py | 263 + tools/rgenetics/rgTDT.xml | 84 + tools/rgenetics/rgTDT_code.py | 43 + tools/rgenetics/rgfakePed.py | 535 ++++ tools/rgenetics/rgfakePed.xml | 111 + tools/rgenetics/rgfakePed_code.py | 53 + tools/rgenetics/rgfakePhe.py | 469 +++ tools/rgenetics/rgfakePhe.xml | 132 + tools/rgenetics/rgfakePhe_code.py | 46 + tools/rgenetics/rgutils.py | 281 ++ 160 files changed, 18356 insertions(+), 0 deletions(-) diffs (truncated from 18957 to 3000 lines): diff -r 4906f2302c85 -r cc8a30a0669f .hgignore --- a/.hgignore Fri Mar 26 14:14:40 2010 -0400 +++ b/.hgignore Fri Mar 26 14:42:15 2010 -0400 @@ -1,3 +1,7 @@ +syntax: regexp + +\.svn$ + syntax: glob .hg* diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgCaCotest1_CaCo.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +rs Chr Offset Genop log10Genop Armitagep log10Armitagep Allelep log10Allelep Domp log10Domp +rs2283802 22 21784722 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267000 22 21785366 1.000 0.000000 0.893 0.049197 0.896 0.047450 1.000 0.000000 +rs16997606 22 21794754 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 +rs4820537 22 21794810 1.000 0.000000 0.266 0.575935 0.238 0.623423 1.000 0.000000 +rs3788347 22 21797804 1.000 0.000000 0.528 0.276955 0.518 0.285251 1.000 0.000000 +rs756632 22 21799918 1.000 0.000000 0.847 0.072014 0.838 0.076704 1.000 0.000000 +rs4820539 22 21807970 1.000 0.000000 0.663 0.178618 0.669 0.174704 1.000 0.000000 +rs2283804 22 21820335 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000 +rs2267006 22 21820990 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000 +rs4822363 22 21821000 1.000 0.000000 0.609 0.215311 0.624 0.204815 1.000 0.000000 +rs5751592 22 21827674 1.000 0.000000 0.426 0.370998 0.470 0.328272 1.000 0.000000 +rs5759608 22 21832708 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs5759612 22 21833170 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267009 22 21860168 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267010 22 21864366 1.000 0.000000 0.729 0.137332 0.734 0.134304 1.000 0.000000 +rs5759636 22 21868698 1.000 0.000000 0.215 0.667360 0.228 0.642256 1.000 0.000000 +rs2071436 22 21871488 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267013 22 21875879 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 +rs6003566 22 21889806 1.000 0.000000 0.361 0.442132 0.389 0.409604 1.000 0.000000 +rs2256725 22 21892891 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 +rs12160770 22 21892925 1.000 0.000000 0.594 0.225921 0.597 0.224098 1.000 0.000000 +rs5751611 22 21896019 1.000 0.000000 0.893 0.049246 0.894 0.048565 1.000 0.000000 +rs762601 22 21898858 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 +rs2156921 22 21899063 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 +rs4822375 22 21905642 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgCaCotest1_CaCo_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,46 @@ + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ rgCaCotest1.log ] +Analysis started: Thu Mar 25 21:01:31 2010 + +Options in effect: + --noweb + --bfile /opt/galaxy/test-data/tinywga + --out rgCaCotest1 + --model + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 10 cases, 30 controls and 0 missing +After filtering, 21 males, 19 females, and 0 of unspecified sex +Full-model association tests, minimum genotype count: --cell 5 +Writing full model association results to [ rgCaCotest1.model ] + +Analysis finished: Thu Mar 25 21:01:31 2010 + +###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772 +Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 25/03/2010 21:01:31 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo_topTable.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgCaCotest1_CaCo_topTable.gff Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +track name=rgGLM_TopTable description="rgCaCotest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00 +chr22 rgGLM variation 21785266 21785466 42 . . rs2267000 logp=0.05 +chr22 rgGLM variation 21794654 21794854 249 . . rs16997606 logp=0.29 +chr22 rgGLM variation 21794710 21794910 493 . . rs4820537 logp=0.58 +chr22 rgGLM variation 21797704 21797904 237 . . rs3788347 logp=0.28 +chr22 rgGLM variation 21799818 21800018 61 . . rs756632 logp=0.07 +chr22 rgGLM variation 21807870 21808070 153 . . rs4820539 logp=0.18 +chr22 rgGLM variation 21820235 21820435 44 . . rs2283804 logp=0.05 +chr22 rgGLM variation 21820890 21821090 44 . . rs2267006 logp=0.05 +chr22 rgGLM variation 21820900 21821100 184 . . rs4822363 logp=0.22 +chr22 rgGLM variation 21827574 21827774 317 . . rs5751592 logp=0.37 +chr22 rgGLM variation 21832608 21832808 0 . . rs5759608 logp=-0.00 +chr22 rgGLM variation 21833070 21833270 0 . . rs5759612 logp=-0.00 +chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00 +chr22 rgGLM variation 21864266 21864466 117 . . rs2267010 logp=0.14 +chr22 rgGLM variation 21868598 21868798 571 . . rs5759636 logp=0.67 +chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00 +chr22 rgGLM variation 21875779 21875979 249 . . rs2267013 logp=0.29 +chr22 rgGLM variation 21889706 21889906 378 . . rs6003566 logp=0.44 +chr22 rgGLM variation 21892791 21892991 249 . . rs2256725 logp=0.29 +chr22 rgGLM variation 21892825 21893025 193 . . rs12160770 logp=0.23 +chr22 rgGLM variation 21895919 21896119 42 . . rs5751611 logp=0.05 +chr22 rgGLM variation 21898758 21898958 40 . . rs762601 logp=0.05 +chr22 rgGLM variation 21898963 21899163 40 . . rs2156921 logp=0.05 +chr22 rgGLM variation 21905542 21905742 40 . . rs4822375 logp=0.05 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLM_GLM_topTable.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgGLM_GLM_topTable.gff Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +track name=rgGLM_TopTable description="rgGLMtest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgGLM variation 21784622 21784822 455 . . rs2283802 logp=0.75 +chr22 rgGLM variation 21785266 21785466 152 . . rs2267000 logp=0.25 +chr22 rgGLM variation 21794654 21794854 230 . . rs16997606 logp=0.38 +chr22 rgGLM variation 21794710 21794910 107 . . rs4820537 logp=0.18 +chr22 rgGLM variation 21797704 21797904 28 . . rs3788347 logp=0.05 +chr22 rgGLM variation 21799818 21800018 45 . . rs756632 logp=0.08 +chr22 rgGLM variation 21807870 21808070 151 . . rs4820539 logp=0.25 +chr22 rgGLM variation 21820235 21820435 723 . . rs2283804 logp=1.19 +chr22 rgGLM variation 21820890 21821090 723 . . rs2267006 logp=1.19 +chr22 rgGLM variation 21820900 21821100 340 . . rs4822363 logp=0.56 +chr22 rgGLM variation 21827574 21827774 337 . . rs5751592 logp=0.55 +chr22 rgGLM variation 21832608 21832808 563 . . rs5759608 logp=0.92 +chr22 rgGLM variation 21833070 21833270 563 . . rs5759612 logp=0.92 +chr22 rgGLM variation 21860068 21860268 455 . . rs2267009 logp=0.75 +chr22 rgGLM variation 21864266 21864466 391 . . rs2267010 logp=0.64 +chr22 rgGLM variation 21868598 21868798 95 . . rs5759636 logp=0.16 +chr22 rgGLM variation 21871388 21871588 455 . . rs2071436 logp=0.75 +chr22 rgGLM variation 21875779 21875979 32 . . rs2267013 logp=0.05 +chr22 rgGLM variation 21889706 21889906 125 . . rs6003566 logp=0.21 +chr22 rgGLM variation 21892791 21892991 32 . . rs2256725 logp=0.05 +chr22 rgGLM variation 21892825 21893025 127 . . rs12160770 logp=0.21 +chr22 rgGLM variation 21895919 21896119 126 . . rs5751611 logp=0.21 +chr22 rgGLM variation 21898758 21898958 446 . . rs762601 logp=0.73 +chr22 rgGLM variation 21898963 21899163 446 . . rs2156921 logp=0.73 +chr22 rgGLM variation 21905542 21905742 446 . . rs4822375 logp=0.73 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLMtest1_GLM.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgGLMtest1_GLM.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +rs chrom offset ADD_stat ADD_p ADD_log10p +rs2283802 22 21784722 1.369 0.1789 0.747390 +rs2267000 22 21785366 0.5866 0.5609 0.251115 +rs16997606 22 21794754 -0.8178 0.4185 0.378305 +rs4820537 22 21794810 0.4346 0.6663 0.176330 +rs3788347 22 21797804 -0.1292 0.8979 0.046772 +rs756632 22 21799918 0.202 0.841 0.075204 +rs4820539 22 21807970 0.5836 0.563 0.249492 +rs2283804 22 21820335 -1.902 0.0648 1.188425 +rs2267006 22 21820990 -1.902 0.0648 1.188425 +rs4822363 22 21821000 1.105 0.2761 0.558934 +rs5751592 22 21827674 1.099 0.2788 0.554707 +rs5759608 22 21832708 -1.596 0.1189 0.924818 +rs5759612 22 21833170 -1.596 0.1189 0.924818 +rs2267009 22 21860168 1.369 0.1789 0.747390 +rs2267010 22 21864366 -1.227 0.2276 0.642828 +rs5759636 22 21868698 0.3942 0.6957 0.157578 +rs2071436 22 21871488 1.369 0.1789 0.747390 +rs2267013 22 21875879 -0.1449 0.8855 0.052811 +rs6003566 22 21889806 -0.4952 0.6233 0.205303 +rs2256725 22 21892891 -0.1449 0.8855 0.052811 +rs12160770 22 21892925 0.5031 0.618 0.209012 +rs5751611 22 21896019 0.5008 0.6195 0.207959 +rs762601 22 21898858 1.35 0.1849 0.733063 +rs2156921 22 21899063 1.35 0.1849 0.733063 +rs4822375 22 21905642 1.35 0.1849 0.733063 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLMtest1_GLM_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgGLMtest1_GLM_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,58 @@ +rgGLM.py called with ['/opt/galaxy/tools/rgenetics/rgGLM.py', '/opt/galaxy/test-data/tinywga', '/opt/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/opt/galaxy/test-data/rgGLMtest1_GLM.xls', '/opt/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/opt/galaxy/test-data/rgGLM_GLM_topTable.gff'] +vcl=['plink', '--noweb', '--bfile', '/opt/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/opt/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] +xformQassoc got resf=/tmp/tmpCB6CwWrgGLM/tinywga.assoc.linear, outfname=/opt/galaxy/test-data/rgGLMtest1_GLM.xls +###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127 + + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ tinywga.log ] +Analysis started: Thu Mar 25 21:01:31 2010 + +Options in effect: + --noweb + --bfile /opt/galaxy/test-data/tinywga + --pheno-name c1 + --pheno /opt/galaxy/test-data/tinywga.pphe + --out tinywga + --mind 1 + --geno 1 + --maf 0 + --linear + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Reading alternate phenotype from [ /opt/galaxy/test-data/tinywga.pphe ] +40 individuals with non-missing alternate phenotype +Assuming a quantitative trait +Missing phenotype value is -9 +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 40 individuals with non-missing status +After filtering, 21 males, 19 females, and 0 of unspecified sex +Converting data to Individual-major format +Writing linear model association results to [ tinywga.assoc.linear ] + +Analysis finished: Thu Mar 25 21:01:31 2010 + diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgQQtest1.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgQQtest1.pdf Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,384 @@ +%PDF-1.4 +%âãÏÓ\r +1 0 obj +<< +/CreationDate (D:20100325210132) +/ModDate (D:20100325210132) +/Title (R 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-log10TDTp AbsTDTOR TDTOR +rs2283802 22 21784722 4 2 4 4 0 1 -0.000000 1 1 +rs2267000 22 21785366 4 2 4 5 0.1111 0.7389 0.131414 1.250000 0.8 +rs16997606 22 21794754 1 3 3 3 0 1 -0.000000 1 1 +rs4820537 22 21794810 1 3 3 6 1 0.3173 0.498530 2.000000 0.5 +rs3788347 22 21797804 3 1 5 4 0.1111 0.7389 0.131414 1.25 1.25 +rs756632 22 21799918 4 2 2 1 0.3333 0.5637 0.248952 2 2 +rs4820539 22 21807970 1 3 4 5 0.1111 0.7389 0.131414 1.250000 0.8 +rs2283804 22 21820335 1 2 5 3 0.5 0.4795 0.319211 1.667 1.667 +rs2267006 22 21820990 3 1 5 3 0.5 0.4795 0.319211 1.667 1.667 +rs4822363 22 21821000 4 2 1 1 0 1 -0.000000 1 1 +rs5751592 22 21827674 4 2 2 5 1.286 0.2568 0.590405 2.500000 0.4 +rs5759608 22 21832708 2 4 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs5759612 22 21833170 3 1 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs2267009 22 21860168 3 4 4 4 0 1 -0.000000 1 1 +rs2267010 22 21864366 3 1 1 1 0 1 -0.000000 1 1 +rs5759636 22 21868698 4 2 0 1 1 0.3173 0.498530 0 0 +rs2071436 22 21871488 4 2 4 4 0 1 -0.000000 1 1 +rs2267013 22 21875879 3 1 3 1 1 0.3173 0.498530 3 3 +rs6003566 22 21889806 3 1 3 2 0.2 0.6547 0.183958 1.5 1.5 +rs2256725 22 21892891 2 1 3 1 1 0.3173 0.498530 3 3 +rs5751611 22 21896019 2 4 8 5 0.6923 0.4054 0.392116 1.6 1.6 +rs762601 22 21898858 1 3 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs2156921 22 21899063 3 1 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs4822375 22 21905642 1 3 7 4 0.8182 0.3657 0.436875 1.75 1.75 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgTDTtest1_TDT_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,53 @@ + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ rgTDTtest1.log ] +Analysis started: Thu Mar 25 21:01:31 2010 + +Options in effect: + --noweb + --bfile /opt/galaxy/test-data/tinywga + --out rgTDTtest1 + --mind 0.5 + --tdt + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +0 of 40 individuals removed for low genotyping ( MIND > 0.5 ) +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 10 cases, 30 controls and 0 missing +After filtering, 21 males, 19 females, and 0 of unspecified sex +14 nuclear families, 1 founder singletons found +13 non-founders with 2 parents in 13 nuclear families +0 non-founders without 2 parents in 0 nuclear families +10 affected offspring trios +0 phenotypically discordant parent pairs found +Converting data to Individual-major format +0 Mendel errors detected in total +Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] + +Analysis finished: Thu Mar 25 21:01:31 2010 + +###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT_topTable.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgTDTtest1_TDT_topTable.gff Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,25 @@ +track name=rgTDT_Top_Table description="rgTDTtest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00 +chr22 rgGLM variation 21785266 21785466 120 . . rs2267000 logp=0.13 +chr22 rgGLM variation 21794654 21794854 0 . . rs16997606 logp=-0.00 +chr22 rgGLM variation 21794710 21794910 457 . . rs4820537 logp=0.50 +chr22 rgGLM variation 21797704 21797904 120 . . rs3788347 logp=0.13 +chr22 rgGLM variation 21799818 21800018 228 . . rs756632 logp=0.25 +chr22 rgGLM variation 21807870 21808070 120 . . rs4820539 logp=0.13 +chr22 rgGLM variation 21820235 21820435 292 . . rs2283804 logp=0.32 +chr22 rgGLM variation 21820890 21821090 292 . . rs2267006 logp=0.32 +chr22 rgGLM variation 21820900 21821100 0 . . rs4822363 logp=-0.00 +chr22 rgGLM variation 21827574 21827774 541 . . rs5751592 logp=0.59 +chr22 rgGLM variation 21832608 21832808 400 . . rs5759608 logp=0.44 +chr22 rgGLM variation 21833070 21833270 400 . . rs5759612 logp=0.44 +chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00 +chr22 rgGLM variation 21864266 21864466 0 . . rs2267010 logp=-0.00 +chr22 rgGLM variation 21868598 21868798 457 . . rs5759636 logp=0.50 +chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00 +chr22 rgGLM variation 21875779 21875979 457 . . rs2267013 logp=0.50 +chr22 rgGLM variation 21889706 21889906 168 . . rs6003566 logp=0.18 +chr22 rgGLM variation 21892791 21892991 457 . . rs2256725 logp=0.50 +chr22 rgGLM variation 21895919 21896119 359 . . rs5751611 logp=0.39 +chr22 rgGLM variation 21898758 21898958 400 . . rs762601 logp=0.44 +chr22 rgGLM variation 21898963 21899163 400 . . rs2156921 logp=0.44 +chr22 rgGLM variation 21905542 21905742 400 . . rs4822375 logp=0.44 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.bed Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,1 @@ +l
ÿëþ¿¾+ê󪿊üŠ £ïªîþ¨êÿïªûÿÿÿÿÿÿþﮨª"ë€ú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿Ÿþ¿ÿëþ¿¾+ê󪿺ûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯Žü(:ú¢ÿ¿«¯Žü(:ú¢ÿ¿«¯Žü(:ú¢ÿ¿«¯Žü( \ No newline at end of file diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.bim Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,25 @@ +22 rs2283802 0 21784722 4 2 +22 rs2267000 0 21785366 4 2 +22 rs16997606 0 21794754 1 3 +22 rs4820537 0 21794810 1 3 +22 rs3788347 0 21797804 3 1 +22 rs756632 0 21799918 4 2 +22 rs4820539 0 21807970 1 3 +22 rs2283804 0 21820335 1 2 +22 rs2267006 0 21820990 3 1 +22 rs4822363 0 21821000 4 2 +22 rs5751592 0 21827674 4 2 +22 rs5759608 0 21832708 2 4 +22 rs5759612 0 21833170 3 1 +22 rs2267009 0 21860168 3 4 +22 rs2267010 0 21864366 3 1 +22 rs5759636 0 21868698 4 2 +22 rs2071436 0 21871488 4 2 +22 rs2267013 0 21875879 3 1 +22 rs6003566 0 21889806 3 1 +22 rs2256725 0 21892891 2 1 +22 rs12160770 0 21892925 1 3 +22 rs5751611 0 21896019 2 4 +22 rs762601 0 21898858 1 3 +22 rs2156921 0 21899063 3 1 +22 rs4822375 0 21905642 1 3 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.fam Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,40 @@ +101 1 3 2 2 2 +101 2 0 0 2 1 +101 3 0 0 1 1 +105 1 3 2 2 2 +105 2 0 0 2 1 +105 3 0 0 1 1 +112 1 3 2 1 2 +112 2 0 0 2 1 +112 3 0 0 1 1 +117 1 3 2 2 2 +117 2 0 0 2 1 +117 3 0 0 1 1 +12 1 3 2 1 2 +12 2 0 0 2 1 +12 3 0 0 1 1 +13 1 3 2 1 2 +13 2 0 0 2 1 +13 3 0 0 1 1 +1334 1 10 11 1 2 +1334 10 0 0 1 1 +1334 11 0 0 2 1 +1334 12 0 0 1 1 +1334 13 0 0 2 1 +1334 2 12 13 2 2 +1340 1 9 10 1 2 +1340 10 0 0 2 1 +1340 11 0 0 1 1 +1340 12 0 0 2 1 +1340 2 11 12 2 2 +1340 9 0 0 1 1 +1341 1 11 12 1 1 +1341 11 0 0 1 1 +1341 12 0 0 2 1 +1341 13 0 0 1 1 +1341 14 0 0 2 1 +1341 2 13 14 2 1 +1344 1 12 13 1 1 +1344 12 0 0 1 1 +1344 13 0 0 2 1 +1345 12 0 0 1 1 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.log Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,66 @@ +rgClean.py started, called as /opt/galaxy/tools/rgenetics/rgClean.py /opt/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /opt/galaxy/test-data/rgtestouts/rgClean 0 0 0 0 + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] +Analysis started: Thu Mar 25 21:01:24 2010 + +Options in effect: +--noweb +--bfile /opt/galaxy/test-data/tinywga +--make-bed +--out /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 +--set-hh-missing +--mind 1 +--geno 1 +--maf 0 +--hwe 0 +--me 1 1 + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +0 markers to be excluded based on HWE test ( p <= 0 ) +0 markers failed HWE test in cases +0 markers failed HWE test in controls +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 10 cases, 30 controls and 0 missing +After filtering, 21 males, 19 females, and 0 of unspecified sex +14 nuclear families, 1 founder singletons found +13 non-founders with 2 parents in 13 nuclear families +0 non-founders without 2 parents in 0 nuclear families +10 affected offspring trios +0 phenotypically discordant parent pairs found +Converting data to Individual-major format +Filtering SNPs/families for Mendel Error rates above 1, 1 +0 Mendel errors detected in total +0 families ( 0 individuals ) removed due to Mendel errors +0 markers removed due to Mendel errors, 25 remaining +Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] +Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] +Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] +Using (default) SNP-major mode +Converting data to SNP-major format + +Analysis finished: Thu Mar 25 21:01:24 2010 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.pbed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.pbed Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgClean.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<ul> +<li><a href="rgCleantest1.bed">rgCleantest1.bed</a></li> +<li><a href="rgCleantest1.bim">rgCleantest1.bim</a></li> +<li><a href="rgCleantest1.fam">rgCleantest1.fam</a></li> +<li><a href="rgCleantest1.log">rgCleantest1.log</a></li> +<li><a href="rgCleantest1.pbed">rgCleantest1.pbed</a></li> +</ul> +</ul></br></div></body></html> \ No newline at end of file diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/Rplots.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/Rplots.pdf Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,59 @@ +%PDF-1.4 +%âãÏÓ\r +1 0 obj +<< +/CreationDate (D:20100325210125) +/ModDate (D:20100325210125) +/Title (R Graphics Output) +/Producer (R 2.10.1) +/Creator (R) +>> +endobj +2 0 obj +<< +/Type /Catalog +/Pages 3 0 R +>> +endobj +3 0 obj +<< +/Type /Pages +/Kids [ +] +/Count 0 +/MediaBox [0 0 504 504] +>> +endobj +4 0 obj +<< +/ProcSet [/PDF /Text] +/Font <<>> +/ExtGState << >> +>> +endobj +5 0 obj +<< +/Type /Encoding +/BaseEncoding /WinAnsiEncoding +/Differences [ 45/minus 96/quoteleft +144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent +/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +>> +endobj +xref +0 6 +0000000000 65535 f +0000000021 00000 n +0000000164 00000 n +0000000213 00000 n +0000000290 00000 n +0000000361 00000 n +trailer +<< +/Size 6 +/Info 1 0 R +/Root 2 0 R +>> +startxref +618 +%%EOF diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,19 @@ +llist=c("Control","Case") +glist=c(2,3) +par(lab=c(10,10,10)) +par(mai=c(1,1,1,0.5)) +pdf("rgEigPCAtest1_PCAPlot.pdf",h=8,w=10) +par(lab=c(10,10,10)) +pca1 = c(0.127600,0.027200,0.145200,0.088700,-0.002600,-0.245300,-0.241200,0.035800,0.290500,0.160700,0.167500,0.027200,0.027200,-0.087000,-0.063000,-0.188600,0.026800,-0.064300,0.092700,-0.241200,0.005600,0.026100,-0.160800,-0.160800,0.026100,0.074200,0.030200,-0.249300,0.183300,-0.102700,0.231200,-0.245300,-0.245300,-0.245300,0.301500,0.030200,0.030200,0.259300) +pca2 = c(0.006000,-0.179400,0.266600,0.076500,-0.036700,-0.016500,0.253700,-0.176600,0.081100,-0.124700,0.041800,-0.179400,-0.179400,0.015400,-0.265600,-0.025100,-0.000800,0.041800,-0.221000,0.253700,-0.205100,-0.035400,-0.034900,-0.034900,-0.035400,0.081900,0.234800,-0.286700,0.120600,0.293900,-0.180800,-0.016500,-0.016500,-0.016500,0.215900,0.234800,0.234800,-0.191600) +pgvec = c(2,2,3,2,2,3,2,2,3,2,2,3,2,2,3,2,2,3,2,2,2,2,3,2,2,2,3,2,2,2,2,2,2,2,2,2,2,2) +plot(pca1,pca2,type='p',main='rgEigPCAtest1', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) +legend("top",legend=llist,pch=glist,col=glist,title="Sample") +grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") +dev.off() +png("rgEigPCAtest1_PCAPlot.pdf.png",h=8,w=10,units="in",res=72) +plot(pca1,pca2,type='p',main='rgEigPCAtest1', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) +legend("top",legend=llist,pch=glist,col=glist,title="Sample") +grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") +dev.off() +#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:25 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,160 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgEigPCA.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<h4>Output from rgEigPCA.py run at 25/03/2010 21:01:25<br/> +</h4> +newfilepath=/opt/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> +<a href="rgEigPCAtest1_PCAPlot.pdf"><img src="rgEigPCAtest1_PCAPlot.pdf.png" alt="Samples plotted in first 2 eigenvector space" hspace="10" align="left" /></a></td></tr></table><br/> +<div class="document">All Files:<ol><li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> +<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (311 B)</a></li> +<li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li> +<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.0 KB)</a></li> +<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> +<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt (257 B)</a></li> +<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps (13.6 KB)</a></li> +<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.3 KB)</a></li> +<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (7.9 KB)</a></li> +<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf (2.1 KB)</a></li> +<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> +<li><a href="Rplots.pdf">Rplots.pdf (813 B)</a></li> +</ol></div><div class="document">Log rgEigPCAtest1_log.txt contents follow below<p/><pre>parameter file: rgEigPCAtest1_pca.xls.par +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +genotypename: /opt/galaxy/test-data/tinywga.ped +snpname: /opt/galaxy/test-data/tinywga.map +indivname: /opt/galaxy/test-data/tinywga.ped +evecoutname: rgEigPCAtest1_pca.xls.evec +evaloutname: rgEigPCAtest1_eval.xls +altnormstyle: NO +numoutevec: 4 +numoutlieriter: 2 +numoutlierevec: 2 +outliersigmathresh: 2 +qtmode: 0 +## smartpca version: 8000 +norm used + +genetic distance set from physical distance +genotype file processed +number of samples used: 40 number of snps used: 25 +REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329 +number of samples after outlier removal: 39 + +## Tracy-Widom statistics: rows: 39 cols: 24 + #N eigenvalue difference twstat p-value effect. n + 1 11.481974 NA -0.712 0.332198 8.854 + 2 7.739771 -3.742203 -1.302 0.510496 8.388 + 3 7.254586 -0.485185 -0.171 0.201072 7.095 + 4 4.270950 -2.983636 -0.191 0.205302 8.005 + 5 2.538320 -1.732630 -0.341 0.238117 9.118 + 6 1.667964 -0.870356 -0.231 0.21376 9.910 + 7 1.043403 -0.624560 -0.269 0.222042 11.590 + 8 0.653401 -0.390003 NA NA NA + 9 0.391044 -0.262357 NA NA NA + 10 0.338164 -0.052880 NA NA NA + 11 0.263384 -0.074780 NA NA NA + 12 0.150750 -0.112634 NA NA NA + 13 0.085580 -0.065170 NA NA NA + 14 0.065301 -0.020279 NA NA NA + 15 0.048797 -0.016504 NA NA NA + 16 0.006611 -0.042186 NA NA NA + kurtosis snps indivs + eigenvector 1 1.926 2.122 + eigenvector 2 2.599 2.148 + eigenvector 3 2.593 2.873 + eigenvector 4 3.165 2.831 +population: 0 Case 9 +population: 1 Control 30 + +## Average divergence between populations: + Case Control popsize + Case 1.028 0.954 9 + Control 0.954 0.972 30 + + +number of blocks for moving block jackknife: 1 +fst *1000: + C C + C 0 0 + C 0 0 + +s.dev * 1000000: + C C + C 0 0 + C 0 0 + +## Anova statistics for population differences along each eigenvector: + p-value + eigenvector_1_Case_Control_ 0.841067 + eigenvector_2_Case_Control_ 0.758376 + eigenvector_3_Case_Control_ 0.238793 + eigenvector_4_Case_Control_ 0.678458 + +## Statistical significance of differences beween populations: + pop1 pop2 chisq p-value |pop1| |pop2| +popdifference: Case Control 1.810 0.77061 9 30 + +eigbestsnp 1 rs762601 22 21898858 1.674 +eigbestsnp 1 rs2156921 22 21899063 1.674 +eigbestsnp 1 rs4822375 22 21905642 1.674 +eigbestsnp 1 rs5751611 22 21896019 1.635 +eigbestsnp 1 rs4820537 22 21794810 1.542 +eigbestsnp 1 rs3788347 22 21797804 1.413 +eigbestsnp 1 rs2267000 22 21785366 1.151 +eigbestsnp 1 rs4820539 22 21807970 1.141 +eigbestsnp 1 rs5751592 22 21827674 0.890 +eigbestsnp 1 rs2283804 22 21820335 0.815 +eigbestsnp 1 rs2267006 22 21820990 0.815 +eigbestsnp 2 rs5759608 22 21832708 2.197 +eigbestsnp 2 rs5759612 22 21833170 2.197 +eigbestsnp 2 rs2283804 22 21820335 1.643 +eigbestsnp 2 rs2267006 22 21820990 1.643 +eigbestsnp 2 rs2283802 22 21784722 1.283 +eigbestsnp 2 rs2267009 22 21860168 1.283 +eigbestsnp 2 rs2071436 22 21871488 1.283 +eigbestsnp 2 rs756632 22 21799918 0.942 +eigbestsnp 2 rs16997606 22 21794754 0.715 +eigbestsnp 2 rs6003566 22 21889806 0.645 +eigbestsnp 2 rs762601 22 21898858 0.545 +eigbestsnp 3 rs16997606 22 21794754 1.770 +eigbestsnp 3 rs6003566 22 21889806 1.725 +eigbestsnp 3 rs3788347 22 21797804 1.452 +eigbestsnp 3 rs2267000 22 21785366 1.386 +eigbestsnp 3 rs2283802 22 21784722 1.247 +eigbestsnp 3 rs2267009 22 21860168 1.247 +eigbestsnp 3 rs2071436 22 21871488 1.247 +eigbestsnp 3 rs4820537 22 21794810 1.168 +eigbestsnp 3 rs762601 22 21898858 1.153 +eigbestsnp 3 rs2156921 22 21899063 1.153 +eigbestsnp 3 rs4822375 22 21905642 1.153 +eigbestsnp 4 rs756632 22 21799918 2.146 +eigbestsnp 4 rs4820539 22 21807970 1.938 +eigbestsnp 4 rs2267013 22 21875879 1.917 +eigbestsnp 4 rs2256725 22 21892891 1.917 +eigbestsnp 4 rs2283804 22 21820335 1.336 +eigbestsnp 4 rs2267006 22 21820990 1.336 +eigbestsnp 4 rs6003566 22 21889806 1.000 +eigbestsnp 4 rs16997606 22 21794754 0.875 +eigbestsnp 4 rs5751611 22 21896019 0.823 +eigbestsnp 4 rs5759636 22 21868698 0.799 +eigbestsnp 4 rs2267000 22 21785366 0.584 +packedancestrymap output +##end of smartpca run + +Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033 +Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051 +Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 +Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 +</pre></div>If you need to rerun this analysis, the command line used was +smartpca.perl -i /opt/galaxy/test-data/tinywga.ped -a /opt/galaxy/test-data/tinywga.map -b /opt/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 +<p/></div></body></html> diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,40 @@ + #eigvals: 11.482 7.740 7.255 4.271 + 101:1 0.1276 0.0060 0.1550 -0.3329 Case + 101:2 0.1276 0.0060 0.1550 -0.3329 Control + 101:3 0.0272 -0.1794 0.3241 -0.0243 Control + 105:1 0.1452 0.2666 -0.0845 -0.3446 Case + 105:2 0.0887 0.0765 0.0527 0.0326 Control + 105:3 -0.0026 -0.0367 -0.1333 -0.2045 Control + 112:1 -0.2453 -0.0165 -0.0856 0.0221 Case + 112:2 -0.2412 0.2537 0.0100 -0.0961 Control + 112:3 0.0358 -0.1766 -0.1010 0.1423 Control + 117:1 0.2905 0.0811 -0.0332 0.2245 Case + 117:2 0.1607 -0.1247 0.1495 0.0759 Control + 117:3 0.1675 0.0418 0.0449 0.2637 Control + 12:1 0.0272 -0.1794 0.3241 -0.0243 Case + 12:2 0.0272 -0.1794 0.3241 -0.0243 Control + 12:3 -0.0870 0.0154 0.2295 -0.1150 Control + 13:1 -0.0630 -0.2656 0.1607 -0.0055 Case + 13:2 -0.1886 -0.0251 -0.0558 -0.0102 Control + 13:3 0.0268 -0.0008 0.3404 -0.0369 Control + 1334:1 -0.0643 0.0418 0.0358 0.0343 Case + 1334:10 0.0927 -0.2210 -0.1938 -0.0651 Control + 1334:11 -0.2412 0.2537 0.0100 -0.0961 Control + 1334:12 0.0056 -0.2051 -0.2132 -0.1240 Control + 1334:13 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:1 -0.1608 -0.0349 0.0222 0.1244 Case + 1340:10 -0.1608 -0.0349 0.0222 0.1244 Control + 1340:11 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:12 0.0742 0.0819 -0.0833 -0.0528 Control + 1340:2 0.0302 0.2348 0.0136 0.1216 Case + 1340:9 -0.2493 -0.2867 -0.1811 0.1404 Control + 1341:1 0.1833 0.1206 -0.1248 -0.0491 Control + 1341:11 -0.1027 0.2939 -0.1091 -0.1832 Control + 1341:12 0.2312 -0.1808 -0.3129 -0.1522 Control + 1341:13 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:14 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:2 -0.2453 -0.0165 -0.0856 0.0221 Control + 1344:1 0.3015 0.2159 0.0173 0.3393 Control + 1344:12 0.0302 0.2348 0.0136 0.1216 Control + 1344:13 0.0302 0.2348 0.0136 0.1216 Control + 1345:12 0.2593 -0.1916 -0.2862 -0.1609 Control diff -r 4906f2302c85 -r cc8a30a0669f 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+0 -5040 translate +0 setgray +newpath +(Helvetica) findfont 140 scalefont setfont +1.000 UL +LTb +714 420 M +63 0 V +6185 0 R +-63 0 V +630 420 M +(-0.3) Rshow +1.000 UL +LTb +714 1162 M +63 0 V +6185 0 R +-63 0 V +-6269 0 R +(-0.2) Rshow +1.000 UL +LTb +714 1904 M +63 0 V +6185 0 R +-63 0 V +-6269 0 R +(-0.1) Rshow +1.000 UL +LTb +714 2646 M +63 0 V +6185 0 R +-63 0 V +-6269 0 R +( 0) Rshow +1.000 UL +LTb +714 3388 M +63 0 V +6185 0 R +-63 0 V +-6269 0 R +( 0.1) Rshow +1.000 UL +LTb +714 4130 M +63 0 V +6185 0 R +-63 0 V +-6269 0 R +( 0.2) Rshow +1.000 UL +LTb +714 4872 M +63 0 V +6185 0 R +-63 0 V +-6269 0 R +( 0.3) Rshow +1.000 UL +LTb +714 420 M +0 63 V +0 4389 R +0 -63 V +714 280 M +(-0.3) Cshow +1.000 UL +LTb +1607 420 M +0 63 V +0 4389 R +0 -63 V +0 -4529 R +(-0.2) Cshow +1.000 UL +LTb +2499 420 M +0 63 V +0 4389 R +0 -63 V +0 -4529 R +(-0.1) Cshow +1.000 UL +LTb +3392 420 M +0 63 V +0 4389 R +0 -63 V +0 -4529 R +( 0) Cshow +1.000 UL +LTb +4284 420 M +0 63 V +0 4389 R +0 -63 V +0 -4529 R +( 0.1) Cshow +1.000 UL +LTb +5177 420 M +0 63 V +0 4389 R +0 -63 V +0 -4529 R +( 0.2) Cshow +1.000 UL +LTb +6069 420 M +0 63 V +0 4389 R +0 -63 V +0 -4529 R +( 0.3) Cshow +1.000 UL +LTb +6962 420 M +0 63 V +0 4389 R +0 -63 V +0 -4529 R +( 0.4) Cshow +1.000 UL +LTb +1.000 UL +LTb +714 420 M +6248 0 V +0 4452 V +-6248 0 V +714 420 L +LTb +140 2646 M +currentpoint gsave translate 90 rotate 0 0 M +(eigenvector 2) Cshow +grestore +LTb +3838 70 M +(eigenvector 1) Cshow +1.000 UP +1.000 UP +1.000 UL +LT0 +LTb +6311 4739 M +(Case) Rshow +LT0 +4531 2691 Pls +4688 4624 Pls +1202 2524 Pls +5985 3248 Pls +3634 1315 Pls +2829 675 Pls +2818 2956 Pls +1956 2387 Pls +3661 4388 Pls +6594 4739 Pls +1.000 UP +1.000 UL +LT1 +LTb +6311 4599 M +(Control) Rshow +LT1 +4531 2691 Crs +3634 1315 Crs +4183 3214 Crs +3369 2374 Crs +1239 4528 Crs +3711 1336 Crs +4826 1721 Crs +4887 2956 Crs +3634 1315 Crs +2615 2760 Crs +1708 2460 Crs +3631 2640 Crs +4219 1006 Crs +1239 4528 Crs +3442 1124 Crs +3625 2383 Crs +1956 2387 Crs +3625 2383 Crs +4054 3254 Crs +1167 519 Crs +5028 3541 Crs +2475 4827 Crs +5455 1304 Crs +1202 2524 Crs +1202 2524 Crs +1202 2524 Crs +6083 4248 Crs +3661 4388 Crs +3661 4388 Crs +5706 1224 Crs +6594 4599 Crs +1.000 UL +LTb +714 420 M +6248 0 V +0 4452 V +-6248 0 V +714 420 L +1.000 UP +stroke +grestore +end +showpage +%%Trailer +%%DocumentFonts: Helvetica +%%Pages: 1 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,7 @@ +set terminal postscript color +set title "" +set xlabel "eigenvector 1" +set ylabel "eigenvector 2" +plot "rgEigPCAtest1_pca.xls.evec.1:2:Case" using 2:3 title "Case" , \ + "rgEigPCAtest1_pca.xls.evec.1:2:Control" using 2:3 title "Control" +## pause 9999 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,39 @@ + 11.481974 + 7.739771 + 7.254586 + 4.270950 + 2.538320 + 1.667964 + 1.043403 + 0.653401 + 0.391044 + 0.338164 + 0.263384 + 0.150750 + 0.085580 + 0.065301 + 0.048797 + 0.006611 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,128 @@ +parameter file: rgEigPCAtest1_pca.xls.par +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +genotypename: /opt/galaxy/test-data/tinywga.ped +snpname: /opt/galaxy/test-data/tinywga.map +indivname: /opt/galaxy/test-data/tinywga.ped +evecoutname: rgEigPCAtest1_pca.xls.evec +evaloutname: rgEigPCAtest1_eval.xls +altnormstyle: NO +numoutevec: 4 +numoutlieriter: 2 +numoutlierevec: 2 +outliersigmathresh: 2 +qtmode: 0 +## smartpca version: 8000 +norm used + +genetic distance set from physical distance +genotype file processed +number of samples used: 40 number of snps used: 25 +REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329 +number of samples after outlier removal: 39 + +## Tracy-Widom statistics: rows: 39 cols: 24 + #N eigenvalue difference twstat p-value effect. n + 1 11.481974 NA -0.712 0.332198 8.854 + 2 7.739771 -3.742203 -1.302 0.510496 8.388 + 3 7.254586 -0.485185 -0.171 0.201072 7.095 + 4 4.270950 -2.983636 -0.191 0.205302 8.005 + 5 2.538320 -1.732630 -0.341 0.238117 9.118 + 6 1.667964 -0.870356 -0.231 0.21376 9.910 + 7 1.043403 -0.624560 -0.269 0.222042 11.590 + 8 0.653401 -0.390003 NA NA NA + 9 0.391044 -0.262357 NA NA NA + 10 0.338164 -0.052880 NA NA NA + 11 0.263384 -0.074780 NA NA NA + 12 0.150750 -0.112634 NA NA NA + 13 0.085580 -0.065170 NA NA NA + 14 0.065301 -0.020279 NA NA NA + 15 0.048797 -0.016504 NA NA NA + 16 0.006611 -0.042186 NA NA NA + kurtosis snps indivs + eigenvector 1 1.926 2.122 + eigenvector 2 2.599 2.148 + eigenvector 3 2.593 2.873 + eigenvector 4 3.165 2.831 +population: 0 Case 9 +population: 1 Control 30 + +## Average divergence between populations: + Case Control popsize + Case 1.028 0.954 9 + Control 0.954 0.972 30 + + +number of blocks for moving block jackknife: 1 +fst *1000: + C C + C 0 0 + C 0 0 + +s.dev * 1000000: + C C + C 0 0 + C 0 0 + +## Anova statistics for population differences along each eigenvector: + p-value + eigenvector_1_Case_Control_ 0.841067 + eigenvector_2_Case_Control_ 0.758376 + eigenvector_3_Case_Control_ 0.238793 + eigenvector_4_Case_Control_ 0.678458 + +## Statistical significance of differences beween populations: + pop1 pop2 chisq p-value |pop1| |pop2| +popdifference: Case Control 1.810 0.77061 9 30 + +eigbestsnp 1 rs762601 22 21898858 1.674 +eigbestsnp 1 rs2156921 22 21899063 1.674 +eigbestsnp 1 rs4822375 22 21905642 1.674 +eigbestsnp 1 rs5751611 22 21896019 1.635 +eigbestsnp 1 rs4820537 22 21794810 1.542 +eigbestsnp 1 rs3788347 22 21797804 1.413 +eigbestsnp 1 rs2267000 22 21785366 1.151 +eigbestsnp 1 rs4820539 22 21807970 1.141 +eigbestsnp 1 rs5751592 22 21827674 0.890 +eigbestsnp 1 rs2283804 22 21820335 0.815 +eigbestsnp 1 rs2267006 22 21820990 0.815 +eigbestsnp 2 rs5759608 22 21832708 2.197 +eigbestsnp 2 rs5759612 22 21833170 2.197 +eigbestsnp 2 rs2283804 22 21820335 1.643 +eigbestsnp 2 rs2267006 22 21820990 1.643 +eigbestsnp 2 rs2283802 22 21784722 1.283 +eigbestsnp 2 rs2267009 22 21860168 1.283 +eigbestsnp 2 rs2071436 22 21871488 1.283 +eigbestsnp 2 rs756632 22 21799918 0.942 +eigbestsnp 2 rs16997606 22 21794754 0.715 +eigbestsnp 2 rs6003566 22 21889806 0.645 +eigbestsnp 2 rs762601 22 21898858 0.545 +eigbestsnp 3 rs16997606 22 21794754 1.770 +eigbestsnp 3 rs6003566 22 21889806 1.725 +eigbestsnp 3 rs3788347 22 21797804 1.452 +eigbestsnp 3 rs2267000 22 21785366 1.386 +eigbestsnp 3 rs2283802 22 21784722 1.247 +eigbestsnp 3 rs2267009 22 21860168 1.247 +eigbestsnp 3 rs2071436 22 21871488 1.247 +eigbestsnp 3 rs4820537 22 21794810 1.168 +eigbestsnp 3 rs762601 22 21898858 1.153 +eigbestsnp 3 rs2156921 22 21899063 1.153 +eigbestsnp 3 rs4822375 22 21905642 1.153 +eigbestsnp 4 rs756632 22 21799918 2.146 +eigbestsnp 4 rs4820539 22 21807970 1.938 +eigbestsnp 4 rs2267013 22 21875879 1.917 +eigbestsnp 4 rs2256725 22 21892891 1.917 +eigbestsnp 4 rs2283804 22 21820335 1.336 +eigbestsnp 4 rs2267006 22 21820990 1.336 +eigbestsnp 4 rs6003566 22 21889806 1.000 +eigbestsnp 4 rs16997606 22 21794754 0.875 +eigbestsnp 4 rs5751611 22 21896019 0.823 +eigbestsnp 4 rs5759636 22 21868698 0.799 +eigbestsnp 4 rs2267000 22 21785366 0.584 +packedancestrymap output +##end of smartpca run + +Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033 +Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051 +Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 +Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,45 @@ +4 +11.4820 +7.7400 +7.2550 +4.2710 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.1608 -0.0349 0.0222 0.1244 + -0.1027 0.2939 -0.1091 -0.1832 + 0.2593 -0.1916 -0.2862 -0.1609 + 0.0302 0.2348 0.0136 0.1216 + -0.2453 -0.0165 -0.0856 0.0221 + 0.3015 0.2159 0.0173 0.3393 + -0.1608 -0.0349 0.0222 0.1244 + -0.1027 0.2939 -0.1091 -0.1832 + 0.2593 -0.1916 -0.2862 -0.1609 + -0.2453 -0.0165 -0.0856 0.0221 + -0.2493 -0.2867 -0.1811 0.1404 + 0.3015 0.2159 0.0173 0.3393 + -0.1027 0.2939 -0.1091 -0.1832 + 0.2593 -0.1916 -0.2862 -0.1609 + 0.0302 0.2348 0.0136 0.1216 + -0.2453 -0.0165 -0.0856 0.0221 + -0.2453 -0.0165 -0.0856 0.0221 + 0.3015 0.2159 0.0173 0.3393 + 0.2593 -0.1916 -0.2862 -0.1609 + 0.0302 0.2348 0.0136 0.1216 + 0.2593 -0.1916 -0.2862 -0.1609 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,40 @@ + #eigvals: 11.482 7.740 7.255 4.271 + 101:1 0.1276 0.0060 0.1550 -0.3329 Case + 101:2 0.1276 0.0060 0.1550 -0.3329 Control + 101:3 0.0272 -0.1794 0.3241 -0.0243 Control + 105:1 0.1452 0.2666 -0.0845 -0.3446 Case + 105:2 0.0887 0.0765 0.0527 0.0326 Control + 105:3 -0.0026 -0.0367 -0.1333 -0.2045 Control + 112:1 -0.2453 -0.0165 -0.0856 0.0221 Case + 112:2 -0.2412 0.2537 0.0100 -0.0961 Control + 112:3 0.0358 -0.1766 -0.1010 0.1423 Control + 117:1 0.2905 0.0811 -0.0332 0.2245 Case + 117:2 0.1607 -0.1247 0.1495 0.0759 Control + 117:3 0.1675 0.0418 0.0449 0.2637 Control + 12:1 0.0272 -0.1794 0.3241 -0.0243 Case + 12:2 0.0272 -0.1794 0.3241 -0.0243 Control + 12:3 -0.0870 0.0154 0.2295 -0.1150 Control + 13:1 -0.0630 -0.2656 0.1607 -0.0055 Case + 13:2 -0.1886 -0.0251 -0.0558 -0.0102 Control + 13:3 0.0268 -0.0008 0.3404 -0.0369 Control + 1334:1 -0.0643 0.0418 0.0358 0.0343 Case + 1334:10 0.0927 -0.2210 -0.1938 -0.0651 Control + 1334:11 -0.2412 0.2537 0.0100 -0.0961 Control + 1334:12 0.0056 -0.2051 -0.2132 -0.1240 Control + 1334:13 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:1 -0.1608 -0.0349 0.0222 0.1244 Case + 1340:10 -0.1608 -0.0349 0.0222 0.1244 Control + 1340:11 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:12 0.0742 0.0819 -0.0833 -0.0528 Control + 1340:2 0.0302 0.2348 0.0136 0.1216 Case + 1340:9 -0.2493 -0.2867 -0.1811 0.1404 Control + 1341:1 0.1833 0.1206 -0.1248 -0.0491 Control + 1341:11 -0.1027 0.2939 -0.1091 -0.1832 Control + 1341:12 0.2312 -0.1808 -0.3129 -0.1522 Control + 1341:13 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:14 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:2 -0.2453 -0.0165 -0.0856 0.0221 Control + 1344:1 0.3015 0.2159 0.0173 0.3393 Control + 1344:12 0.0302 0.2348 0.0136 0.1216 Control + 1344:13 0.0302 0.2348 0.0136 0.1216 Control + 1345:12 0.2593 -0.1916 -0.2862 -0.1609 Control diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,11 @@ +genotypename: /opt/galaxy/test-data/tinywga.ped +snpname: /opt/galaxy/test-data/tinywga.map +indivname: /opt/galaxy/test-data/tinywga.ped +evecoutname: rgEigPCAtest1_pca.xls.evec +evaloutname: rgEigPCAtest1_eval.xls +altnormstyle: NO +numoutevec: 4 +numoutlieriter: 2 +numoutlierevec: 2 +outliersigmathresh: 2 +qtmode: 0 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,23 @@ +Reading genotypes for 40 subjects and 25 markers +Calculating 780 pairs, updating every 78 pairs... +Estimated time is 0.00 to 0.00 seconds ... +0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec +0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec +0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec +0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec +0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec +0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec +0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec +0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec +0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec +T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) +Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 +Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 +Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 +Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +780 pairs are available of 780 +Outliers: 0 +Plotting ... \ No newline at end of file diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/rgGRRtest1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,65 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgGRR.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<h4><div>Output from rgGRR.py run at 25/03/2010 21:01:24<br> +</h4> +If you need to rerun this analysis, the command line was +<pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre> +</div> <embed src="rgGRRtest1.svg" type="image/svg+xml" width="1150" height="600" /><div><h4>Click the links below to save output files and plots</h4><br><ol> +<li><a href="rgGRRtest1.svg" type="image/svg+xml" >rgGRR Plot (requires SVG)</a></li> +<li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li> +<li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li> +<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> +</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 25 markers + +Calculating 780 pairs, updating every 78 pairs... + +Estimated time is 0.00 to 0.00 seconds ... + +0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec + +0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec + +0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec + +0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec + +0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec + +0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec + +0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec + +0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec + +0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec + +T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) + +Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 + +Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 + +Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 + +Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +780 pairs are available of 780 + +Outliers: 0 + +Plotting ...</pre><hr></div></body></html> diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/rgGRRtest1.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Fri Mar 26 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