Names of files, in a list format, to be evaluated on the Discovery Environment (DE). There are only three possible input groups for file.list, regular fileset (.map/.ped), transposed fileset (.tfam/.tped), and binary fileset (.bed/.bim/.fam).
file.path
Optional path to a user's subdirectory on the DE; default path is empty, which leads to the home directory
job.name
The name to give the job being submitted
out.basename
The base name for the output files (not including extension).
assoc.method
PLINKs association methods. Choices are outlined on the PLINK below, see details
no.sex
The sex column (5) is all zeroes (No sex field) (default is TRUE)
multi.adjust
Adjustment for multiple testing (recommended). A file of adjust significance values that correct for all tests performed and other metrics will be created (default is TRUE).
args
Optional for arguments (i.e. flags). The PLINK model has so much additional functionality that it cannot all be fit into this wrapper function (http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml#options). This option allows users to add anything that is not included (.i.e. args="–silent"), to suppress output to console, see details.
print.curl
Prints the curl statement that can be used in the terminal, if curl is installed on your computer
shared.username
With iPlant you have the ability to share folders with other users. If someone has shared a folder with you and you want to run a job with them, enter their username for this input.
suppress.Warnings
This will turn off the warnings, will speed up run time. Use with caution, if the inputs are incorrect they will not be caught.
Details
The inputs for file.list are to be used only in three very strict groups. Group 1: TFAM, TPED, these are the PLINK transposed filesets. Group 2: MAP, PED, these are the PLINK regular filesets. Group 3: BED, BIM, FAM, these are the PLINK binary filesets.
‘assoc.method’ lets the user choose the quantitative method. It isn't recommended, but if NONE is selected, that means no method will be done, one can use this to enter something into the command line. All possible arguments to be entered by user for ‘assoc.method’ are outlined below, if a different argument is entered the application will fail.
"assoc.method"
"explanation"
Standard
Standard case/control association analysis
QTM
Quantitative trait means
GxE
Quantitative trait GxE
Fisher
Fisher's exact test
AlternateModel
Alternate/Full model testing
Breslow-Day
Test of homogeneity -- Breslow-Day homogeneity of odds ratio test
Homog
Test of homogeneity -- partitioning chi-square homogeneity of odds ratio test