The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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PLINK

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PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

  • (Required) To use PLINK, input your data in PLINK's .ped and .map format.
  • (Required) Select the appropriate options for your data set.
  • (Required) Select your desired association method.
  • (Optional) Command line extension, script.txt, any options that are not available in this application can be added to the text.
  • (Optional) Select any files that may be used to aid the PLINK process.
  • Resources: http://pngu.mgh.harvard.edu/~purcell/plink/
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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 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 using transposed fileset (.tfam/.tped) 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.

The plink.assoc file is the association results.  There are many other output files that will be created depending on the choices made for the mode.  For the test case, the output files you will find in the example_data directory are named plink.assoc.linear, plink.assoc.linear.adjusted, plink.log and plink.nosex.

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