Hi, Sylvian,
The plink/rgenetics lped and pbed (compressed) formats are special 'composite' Galaxy datatypes because the map and pedigree/genotype files need to be kept together correctly inside Galaxy. As a result, the upload tool requires that the file type be specified so all of the components can be properly uploaded and stored together.
For example, to upload pbed data from your local desktop, choose 'Upload file' from the Get Data tools.
When the upload form appears, the trick is that you *must* change the default 'Autodetect' in the first (filetype) select box to the specific rgenetics datatype - either 'pbed' as the format for compressed plink data (or 'lped' for uncompressed plink genotype data) as the very first step. Type the first few letters into the first box, and select the right one from the list that appears.
Once this is done, you will see that the upload tool form will change to show three separate file upload inputs - one each for the plink xxx.bim xxx.bed and xxx.fam where xxx is the name you set when you ran plink to create the files, or for uncompressed linkage format two separate file upload inputs - the plink .ped and .map files.
Now you can browse for the corresponding file for each input box from your local machine - be careful not to mix them up as the upload tool is unable to tell unfortunately.
At the bottom of the form, I suggest you then change the genome build to the appropriate one (eg hg18 or hg19).
Finally, I'd recommend that you change the 'metadata value for basename' (which will be the new dataset name) to something that will remind you what the data are - something more meaningful than the default 'rgenetics'.
Click 'execute' to upload the data and create the new dataset in your history. Compressed (pbed) format is preferred so the upload is quicker.
Note that some tools will autoconvert between lped and pbed so there is a delay the first time some tools are run on a new dataset. There are built in converters (use the pencil icon) also if you need them.
I hope this helps - thanks for using Galaxy and Rgenetics - please let us know how you go and feel free to contact me if you have other questions.
dear Galaxy users,
I would like to import genotyping data in Rgenetics and I can't succeed.
I have ped file and map file, I try to import them in lped format but it didn't work ...
Anybody with experience can help me to solve this issue ?
Many thanks in advance,
Best regards,
Sylvain
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Ross Lazarus MBBS MPH
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