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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> PLINK.

There is one input format, the standard PLINK format, three possible input formats, only one may be used at a time.   Make sure to follow the directions on the application when entering input data.  For example, if using the regular fileset (.map/.ped) then enter the inputs into .map and .ped box respectively, leaving all other input boxes empty.  If your current file format is one of the alternative forms using transposed fileset (.tfam/.tped, .bed/.bim/.fam), use the PLINK Conversion to convert to the standard PLINK format.  If you have an alternative file format that is not PLINK, then Tassel3 Conversion or Tassel4 Conversion can be used to attain the proper PLINK file format) then enter inputs in the labeled .tfam and .tped boxes, leaving the other boxes empty .  In ADDITION the user must go to the parameters section and check the box saying 'Transposed files are inputs'.  The same thing must be done when entering the binary fileset.

  1. Regular Fileset (.map/.ped).
  2. Transposed Fileset (.tfam/.tped)
  3. Binary Fileset (.bed/.bim/.fam)

    Optional Input Files

When the app is run in the Discovery Environment, use the following parameters can be chosen.  PLINK has numerous parameters that are possible, only the ones that are in the DE application will be discussed on this help page.  Go here to see all possible options for PLINK.