updateGroupIdAndSex: Update group and geneder information

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

Update group and geneder information

Description

Replace group and gender information in the PLINK binary files by using the information from the metadata file.

Usage

updateGroupIdAndSex(plink, inputPrefix, metaDataFile, 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.
metaDataFile	a pure text file that stores the meta information of the samples. This file must contain at least the following content (column names are in parentheses): family ID in the PLINK files (FID), individual ID in the PLINK files (IID), ID in the description files (descID), self identified ancestry (ance; e.g. AFR: African, AMR: Ad Mixed American, EAS: East Asian, EUR: European, SAS: South Asian), sex (sex; 1 = male, 2 = female), age (age), group (group; 0 = control/unaffected, 1 = case/affected). All unknown and missing values are represented by the value NA. Lines with a missing value for FID or IID are not contained.
outputPrefix	the prefix of the output PLINK binary files.

Details

Find the shared sample IDs between PLINK input files and metadata file. Use the information from the metadata file as the reference and update the group information/the outcome in the PLINK file. Group label should be 1 and 2. (1=unaff, 2=aff, 0=miss); missing phenotype will be indicated as -9.

Value

The output PLINK binary files after updating the gender and grouping information.

Author(s)

Junfang Chen

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")
metaDataFile <- system.file("extdata", "1_01_metaData.txt",
                            package="Gimpute")
system(paste0("scp ", bedFile, bimFile, famFile, " ."))
inputPrefix <- "controlData" ## Specify the input PLINK file prefix
outputPrefix <- "1_03_replacedGroupAndSex" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## updateGroupIdAndSex(plink, inputPrefix, metaDataFile, outputPrefix)

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