PLINK: PLINK-1.07
In rPlant: R interface to the Agave and Foundation API

Description Usage Arguments Details Value See Also Examples

PLINK is an open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner, check http://pngu.mgh.harvard.edu/~purcell/plink/ for details.

PLINK(file.list="", file.path="", job.name=NULL, out.basename=NULL,
      association.method="--assoc", no.sex=TRUE, args=NULL,
      print.curl=FALSE, multi.adjust=TRUE, email=TRUE,
      shared.username=NULL, suppress.Warnings=FALSE)

`file.list`	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).
`association.method`	PLINKs association methods. Choices are outlined on the PLINK webpage, http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml
`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.
`email`	By default an email will be sent to the user when the job finishes.

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.

See the PLINK website for more information. http://pngu.mgh.harvard.edu/~purcell/plink

Additional arguments, args, can be found at http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml#options. The args input is text with the flags and inputs for those flags in a string like on the command line.

There are many output files possible, http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml#output

A list containing the job id and the job name is provided for jobs submitted. If an error, then a message stating the error should also be reported.

SubmitJob, Validate, UploadFile

## Not run: data(geno_test.tfam)
## Not run: data(geno_test.tped)
## Not run: write.table(geno_test.tfam, file = "geno_test.tfam", row.names=FALSE, 
                     col.names=FALSE, quote=FALSE, sep="\t")
## End(Not run)
## Not run: write.table(geno_test.tped, file = "geno_test.tped", row.names=FALSE,
                     col.names=FALSE, quote=FALSE, sep="\t")
## End(Not run)
## Not run: Validate("username","password")
## Not run: UploadFile("geno_test.tfam")
## Not run: UploadFile("geno_test.tped")
## Not run: PLINK(file.list=list("geno_test.tfam","geno_test.tped"),
               association.method="--assoc", print.curl=TRUE)
## End(Not run)