PLINKConversion: PLINKConversion

Description Usage Arguments Details Value See Also Examples

View source: R/PLINKConversion.R

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 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.

Usage

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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)

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 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.

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 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

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.

See Also

SubmitJob, Validate, UploadFile

Examples

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## 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")

rPlant documentation built on May 31, 2017, 3:43 a.m.