snp_plinkRmSamples: Remove samples

In bigsnpr: Analysis of Massive SNP Arrays

Remove samples

Description

Create new bed/bim/fam files by removing samples with PLINK.

Usage

snp_plinkRmSamples(
  plink.path,
  bedfile.in,
  bedfile.out,
  df.or.files,
  col.family.ID = 1,
  col.sample.ID = 2,
  ...,
  verbose = TRUE
)

Arguments

plink.path	Path to the executable of PLINK 1.9.
bedfile.in	Path to the input bedfile.
bedfile.out	Path to the output bedfile.
df.or.files	Either A data.frame, A character vector of file names where to find at the information you want. You should have one column for family IDs and one for sample IDs.
col.family.ID	Index of the column containing the family IDs to match with those of the study. Default is the first one.
col.sample.ID	Index of the column containing the sample IDs to match with those of the study. Default is the second one.
...	Any additional parameter to pass to bigreadr::fread2(). Particularly, option header = FALSE is sometimes needed.
verbose	Whether to show PLINK log? Default is TRUE.

Value

The path of the new bedfile.

See Also

download_plink

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.