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Converting PLINK v1.9 data files into PLINK v2.0 data files

Source: R/ancestry.R
convert_to_plink2.Rd

This converts files in the PLINK v1.9 format (i.e. name.bim, name.fam, and name.bed) into PLINK v2.0 format (i.e. name.pvar, name.psam, and name.pgen)

Usage

convert_to_plink2(
  indir,
  name,
  qcdir = indir,
  verbose = FALSE,
  path2plink2 = NULL,
  keep_individuals = NULL,
  remove_individuals = NULL,
  exclude_markers = NULL,
  extract_markers = NULL,
  showPlinkOutput = TRUE
)

Arguments

indir

[character] /path/to/directory containing the basic PLINK 1.9 data file name.bim, name.fam, name.bed

name

[character] Prefix of PLINK 1.9 files, i.e. name.bim, name.fam, name.bed

qcdir

[character] /path/to/directory where the plink2 data formations as returned by plink2 –make-pgen 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').

keep_individuals

[character] Path to file with individuals to be retained in the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples not listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

remove_individuals

[character] Path to file with individuals to be removed from the analysis. The file has to be a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column. All samples listed in this file will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#indiv. Default: NULL, i.e. no filtering on individuals.

exclude_markers

[character] Path to file with makers to be removed from the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All listed variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

extract_markers

[character] Path to file with makers to be included in the analysis. The file has to be a text file with a list of variant IDs (usually one per line, but it's okay for them to just be separated by spaces). All unlisted variants will be removed from the current analysis. See https://www.cog-genomics.org/plink/1.9/filter#snp. Default: NULL, i.e. no filtering on markers.

showPlinkOutput

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

Value

Creates plink 2.0 datafiles

Examples

indir <- system.file("extdata", package="plinkQC")
qcdir <- tempdir()
name <- "data"
path2plink <- '/path/to/plink'
if (FALSE) { # \dontrun{
# the following code is not run on package build, as the path2plink on the
# user system is not known.
convert_to_plink2(indir=indir, qcdir=qcdir, name=name, path2plink2 = path2plink2)
} # }