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
)

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.

The path of the new bedfile.