PLINKConversion: PLINKConversion
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. This function converts the standard PLINK file formats (Regular (ped/map), Transposed (tped/tfam), and Binary (bed/bim/fam)) to various other PLINK file formats.

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PLINKConversion(file.list="", file.path="", output.type="--recode",
                job.name=NULL, shared.username=NULL, print.curl=FALSE,
                 suppress.Warnings=FALSE, out.basename=NULL, email=TRUE)

`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
`output.type`	PLINKs conversion methods. Choices are outlined on the PLINK webpage, see details for more information.
`out.basename`	The base name for the output files (not including extension).
`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.

‘output.type’ gives the user a lot of flexibility by allowing you to type in the proper argument. All possible arguments for ‘output.type’ are outlined below, if a different argument is entered the application will fail.

	"output.type"	"explanation"
[,1]	--make-bed	Make .bed, .fam and .bim
[,2]	--recode	Output new .ped and .map files
[,3]	--recode12	As above, with 1/2 allele coding
[,4]	--recode-rlist	List individuals with minor allele genotypes
[,5]	--recode-lgen	Output data in long LGEN format
[,6]	--recodeHV	As above, with Haploview .info file
[,7]	--recode-fastphase	Ouput fastphase format file
[,8]	--recode-bimbam	Ouput bimbam format file
[,9]	--recode-structure	Ouput structure format file
[,10]	--recodeA	Raw data file with additive coding
[,11]	--recodeAD	Raw data file with additive/dominance coding
[,12]	--recode --transpose	Transposed Filests (.tfam/.tped)

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

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: PLINKConversion(file.list=list(geno_test.tfam, geno_test.tped), output.type="--recode")