Run plink --pca to calculate the principal components on merged genotypes of the study and reference dataset.
run_check_ancestry(indir, prefixMergedDataset, qcdir = indir,
verbose = FALSE, path2plink = NULL, showPlinkOutput = TRUE)
[character] /path/to/directory containing the basic PLINK data files prefixMergedDataset.bim,prefixMergedDataset.fam and prefixMergedDataset.bed.
[character] Prefix of merged study and reference data files, i.e. prefixMergedDataset.bed, prefixMergedDataset.bim, prefixMergedDataset.fam.
[character] /path/to/directory to save prefixMergedDataset.eigenvec as returned by plink --pca. User needs writing permission to qcdir. Per default qcdir=indir.
[logical] If TRUE, progress info is printed to standard out.
[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').
[logical] If TRUE, plink log and error messages are printed to standard out.
Both, run_check_ancestry
and its evaluation by
evaluate_check_ancestry
can simply be invoked by
check_ancestry
.
# 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)
# }
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