plinkQC (version 1.0.0)

rename_variant_identifiers: Renaming variants

Description

Changes the format of the variant identifier. The default is in the format of chr1:12345[hg38].

Usage

rename_variant_identifiers(
  indir,
  name,
  qcdir = indir,
  verbose = FALSE,
  path2plink2 = NULL,
  format = "@:#[hg38]",
  showPlinkOutput = TRUE
)

Value

Files with a .renamed in them that have the renamed variants

Arguments

indir

[character] /path/to/directory containing the basic PLINK 2.0 data file name.pgen, name.pvar, name.psam

name

[character] Prefix of PLINK 2.0 files, i.e. name.pgen, name.pvar, name.psam

qcdir

[character] /path/to/directory where name.sscore as returned by plink2 --score will be saved to. User needs writing permission to qcdir. Per default is qcdir=indir.

verbose

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

path2plink2

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/2.0/) i.e. plink 2 should be accessible 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('plink').

format

[character] This gives the template to rewrite the variant identifier. A '@' represents the chromosome code, and a '#' represents the base-pair position.

showPlinkOutput

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

Examples

indir <- system.file("extdata", package="plinkQC")
qcdir <- tempdir()
name <- "data.hg38"
path2plink <- '/path/to/plink'
if (FALSE) {
# the following code is not run on package build, as the path2plink on the
# user system is not known.
rename_variant_identifiers(indir=indir, qcdir=qcdir, name=name, path2plink2 = path2plink2)
}