details: http://www.bx.psu.edu/hg/galaxy/rev/b1165a0614ff changeset: 3575:b1165a0614ff user: fubar: ross Lazarus at gmail period com date: Sat Mar 27 14:25:10 2010 -0400 description: Change to rgCaCo to output NAs unchanged rather than fiddling with any p values This fixes an ugly artifact detected in manhatten plots Improved fidelity means downstream apps will need to cope with the awful realities diffstat: test-data/rgCaCotest1_CaCo.xls | 50 +++++++++++----------- test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0 3 files changed, 25 insertions(+), 25 deletions(-) diffs (59 lines): diff -r bda77e05c7c0 -r b1165a0614ff test-data/rgCaCotest1_CaCo.xls --- a/test-data/rgCaCotest1_CaCo.xls Sat Mar 27 11:42:45 2010 -0400 +++ b/test-data/rgCaCotest1_CaCo.xls Sat Mar 27 14:25:10 2010 -0400 @@ -1,26 +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 +rs2283802 22 21784722 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267000 22 21785366 NA 0.000000 0.8929 0.049197 0.8965 0.047450 NA 0.000000 +rs16997606 22 21794754 NA 0.000000 0.5119 0.290815 0.54 0.267606 NA 0.000000 +rs4820537 22 21794810 NA 0.000000 0.2655 0.575935 0.238 0.623423 NA 0.000000 +rs3788347 22 21797804 NA 0.000000 0.5285 0.276955 0.5185 0.285251 NA 0.000000 +rs756632 22 21799918 NA 0.000000 0.8472 0.072014 0.8381 0.076704 NA 0.000000 +rs4820539 22 21807970 NA 0.000000 0.6628 0.178618 0.6688 0.174704 NA 0.000000 +rs2283804 22 21820335 NA 0.000000 0.8879 0.051636 0.8914 0.049927 NA 0.000000 +rs2267006 22 21820990 NA 0.000000 0.8879 0.051636 0.8914 0.049927 NA 0.000000 +rs4822363 22 21821000 NA 0.000000 0.6091 0.215311 0.624 0.204815 NA 0.000000 +rs5751592 22 21827674 NA 0.000000 0.4256 0.370998 0.4696 0.328272 NA 0.000000 +rs5759608 22 21832708 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs5759612 22 21833170 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267009 22 21860168 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267010 22 21864366 NA 0.000000 0.7289 0.137332 0.734 0.134304 NA 0.000000 +rs5759636 22 21868698 NA 0.000000 0.2151 0.667360 0.2279 0.642256 NA 0.000000 +rs2071436 22 21871488 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267013 22 21875879 NA 0.000000 0.5119 0.290815 0.54 0.267606 NA 0.000000 +rs6003566 22 21889806 NA 0.000000 0.3613 0.442132 0.3894 0.409604 NA 0.000000 +rs2256725 22 21892891 NA 0.000000 0.5119 0.290815 0.54 0.267606 NA 0.000000 +rs12160770 22 21892925 NA 0.000000 0.5944 0.225921 0.5969 0.224098 NA 0.000000 +rs5751611 22 21896019 NA 0.000000 0.8928 0.049246 0.8942 0.048565 NA 0.000000 +rs762601 22 21898858 NA 0.000000 0.8972 0.047111 0.8932 0.049051 NA 0.000000 +rs2156921 22 21899063 NA 0.000000 0.8972 0.047111 0.8932 0.049051 NA 0.000000 +rs4822375 22 21905642 NA 0.000000 0.8972 0.047111 0.8932 0.049051 NA 0.000000 diff -r bda77e05c7c0 -r b1165a0614ff test-data/rgtestouts/rgManQQ/Allelep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed diff -r bda77e05c7c0 -r b1165a0614ff test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png has changed