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Projecting the study data set onto the PC space of the reference dataset

Source: R/ancestry.R
run_ancestry_prediction.Rd

Projects the study dataset onto the PC space of the reference dataset. The output of this function as input in a random forest classifier to predict the genomic ancestry of the samples. Genomic data version hg38 with variant identifiers in the format of 1:12345[hg38] is needed for ancestry identification to work.

Usage

run_ancestry_prediction(
  indir,
  name,
  qcdir = indir,
  verbose = FALSE,
  path2plink2 = NULL,
  path2load_mat = NULL,
  keep_individuals = NULL,
  remove_individuals = NULL,
  extract_markers = NULL,
  exclude_markers = NULL,
  showPlinkOutput = TRUE
)

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').

path2load_mat

[character] /path/to/directory where loading matrices are kept. This can be downloaded from: https://github.com/meyer-lab-cshl/plinkQCAncestryData. Note that file names before the .acount or .eigenvec.allele must be included in file path.

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.

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.

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.

showPlinkOutput

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

Value

A .sscore file with the input data projected onto the reference data PCs

Examples

indir <- system.file("extdata", package="plinkQC")
qcdir <- tempdir()
name <- "data.hg38"
path2plink <- '/path/to/plink'
path2load_mat <- '/path/to/load_mat/merged_chrs.postQC.train.pca'
if (FALSE) { # \dontrun{
# the following code is not run on package build, as the path2plink on the
# user system is not known.
superpop_classification(indir=indir, qcdir=qcdir, name=name, 
path2plink2 = path2plink2, path2load_mat = path2load_mat)
} # }