Content Comparison

...

Input File(s)

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
   • 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 homoogeneityhomogeneity Breslow-Day homogeneity of odds ratios test
  • Test of homoogeneityhomogeneity partitioning chi-square homogeneity of odds ratio testHotellings's T(s) test
  • Linear model testing
  • Logistic model testing
  • Stratified Analysis, Cochran-Mantel-Haenszel (basic) test (Cluster file REQUIRED)
  • Stratified Analysis, Cochran-Mantel-Haenszel (IxJxK) test(Cluster file REQUIRED)

• Adjustment for multiple testingOptional Files
• Phenotype Files
• Covariate File (for --gxe)
Cluster File
• 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

...