rPlant (version 2.16)

PLINKConversion: PLINKConversion

Description

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 https://pods.iplantcollaborative.org/wiki/display/DEapps/PLINK+Conversion 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.

Usage

PLINKConversion(file.list="", file.path="", output.type="PED/MAP", job.name=NULL, shared.username=NULL, print.curl=FALSE, suppress.Warnings=FALSE, out.basename=NULL)

Arguments

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 output file types. Choices are outlined below, see details.

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.

Value

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.

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.

`output.type' gives the user allows the user to pick what file type to convert the data set to. All possible arguments to be entered by user for `output.type' are outlined below, if a different argument is entered the application will fail.

"output.type"	"explanation"
PED/MAP	Output new .ped and .map files
TFAM/TPED	Transposed Filests (.tfam/.tped)
BED/FAM/BIM	Make .bed, .fam and .bim
LGEN	Output data in long LGEN format
RAWa	Raw data file with additive coding
RAWad	Raw data file with additive/dominance coding
PED/MAP-1/2	Regular fileset (.map/.ped) with 1/2 allele coding
FASTPHASE	Ouput fastphase format file
BIMBAM	Ouput bimbam format file
STRUCTURE	Ouput structure format file

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

See Also

SubmitJob, Validate, UploadFile

Examples

## 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="BED/FAM/BIM")## End(Not run)