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.

Quick Start

• (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/

Test Data

Input File(s)

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
   • Phenotype Files
   • Covariate File

Parameters Used in App

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.

• Fileset Options.  The basic (.map/.ped) input file format may not be the default format described on the webpage.  If there are any changes from the original make sure to highlight them.
• Association Method.
  • Standard case/control association analysis
  • Quantitative trait means
  • Quantitative trait GxE
  • Fisher's exact test
  • Alternate/Full model testing
  • Fisher's exact full model test
  • Test of homogeneity Breslow-Day homogeneity of odds ratios test
  • Test of homogeneity partitioning chi-square homogeneity of odds ratio test
  • Linear model testing
  • Logistic model testing

• Adjustment for multiple testing
• Command Line Extension. A simple text file that you can write that has custom options not available on the DE.
• Output file name. Enter output BASE file name

Output File(s)

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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