bigsnpr: snp_plinkRmSamples – R documentation

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snp_plinkRmSamples

Remove samples

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

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

`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 second one.
`col.sample.ID`	Index of the column containing the sample IDs to match with those of the study. Default is the first 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`.

The path of the new bedfile.