plink_subset: Subset samples and variants using PLINK
In imbs-hl/imbs: Collection of functions used at the IMBS

Description Usage Arguments Details Value

Subset samples and variants using PLINK

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plink_subset(bfile, output.prefix, remove, keep, exclude, extract, ...,
  bed.file = NULL, bim.file = NULL, fam.file = NULL,
  exec = "plink2", num.threads, memory)

`bfile`	[`string`] The basename of the binary PLINK files.
`output.prefix`	[`string`] The basename of the new binary PLINK files.
`remove`	[`string`] File name of a list of sample FIDs and IIDs to remove.
`keep`	[`string`] File name of a list of sample FIDs and IIDs to keep.
`exclude`	[`string`] File name of a list of variant names to remove.
`extract`	[`string`] File name of a list of variant names to keep.
`...`	[`character`] Additional arguments passed to PLINK.
`bed.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`bim.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`fam.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`exec`	[`string`] Path of PLINK executable.
`num.threads`	[`int`] Number of CPUs usable by PLINK. Default is determined by SLURM environment variables and at least 1.
`memory`	[`int`] Memory for PLINK in Mb. Default is determined by minimum of SLURM environment variables `SLURM_MEM_PER_CPU` and `num.threads * SLURM_MEM_PER_NODE` and at least 5000.