updatedSnpInfo: Update the SNP information

In transbioZI/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline

Update the SNP information

Description

Update SNP information including SNP name, base-pair position, chromosomal location and the strand information.

Usage

updatedSnpInfo(plink, inputPrefix, chipAnnoFile, chipType, outputPrefix)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
inputPrefix	the prefix of the input PLINK binary files.
chipAnnoFile	a pure text file that stores the chip annotation information. If the chip annotation file is not available for your study, it can be downloaded from http://www.well.ox.ac.uk/~wrayner/strand/.
chipType	a string name defines the type of the chip annotation file: 'SNPIDstudy', and 'rsIDstudy'. The detail is described in prepareAnnoFile4affy.
outputPrefix	the prefix of the output PLINK binary files.

Details

The SNP information in the chip annotation file is used as the reference.

Value

The output PLINK binary files after updating SNP information.

Author(s)

Junfang Chen

See Also

prepareAnnoFile4affy

Examples

## In the current working directory
bedFile <- system.file("extdata", "controlData.bed", package="Gimpute")
bimFile <- system.file("extdata", "controlData.bim", package="Gimpute") 
famFile <- system.file("extdata", "controlData.fam", package="Gimpute")
chipAnnoFile <- system.file("extdata", "chipAnno.txt", package="Gimpute")
system(paste0("scp ", bedFile, bimFile, famFile, " ."))
inputPrefix <- "controlData"     
chipType <- "rsIDstudy"
outputPrefix <- "updatedSnpInfo"
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## updatedSnpInfo(plink, inputPrefix, chipAnnoFile, 
##                chipType, outputPrefix, outputSNPfile)

transbioZI/Gimpute documentation built on April 10, 2022, 4:20 a.m.