plinkQC (version 0.2.2)

run_check_ancestry: Run PLINK principal component analysis

Description

Run plink --pca to calculate the principal components on merged genotypes of the study and reference dataset.

Usage

run_check_ancestry(indir, prefixMergedDataset, qcdir = indir,
  verbose = FALSE, path2plink = NULL, showPlinkOutput = TRUE)

Arguments

indir

[character] /path/to/directory containing the basic PLINK data files prefixMergedDataset.bim,prefixMergedDataset.fam and prefixMergedDataset.bed.

prefixMergedDataset

[character] Prefix of merged study and reference data files, i.e. prefixMergedDataset.bed, prefixMergedDataset.bim, prefixMergedDataset.fam.

qcdir

[character] /path/to/directory to save prefixMergedDataset.eigenvec as returned by plink --pca. User needs writing permission to qcdir. Per default qcdir=indir.

verbose

[logical] If TRUE, progress info is printed to standard out.

path2plink

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accesible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec_wait('plink').

showPlinkOutput

[logical] If TRUE, plink log and error messages are printed to standard out.

Details

Both, run_check_ancestry and its evaluation by evaluate_check_ancestry can simply be invoked by check_ancestry.

Examples

# NOT RUN {
indir <- system.file("extdata", package="plinkQC")
qcdir <- tempdir()
prefixMergedDataset <- 'data.HapMapIII'
# the following code is not run on package build, as the path2plink on the
# user system is not known.
# }
# NOT RUN {
run <- run_check_ancestry(indir=indir, qcdir=qcdir, prefixMergedDataset)
# }