plink_ld_pruning: LD pruning with PLINK
In imbs-hl/imbs: Collection of functions used at the IMBS

Description Usage Arguments Details Value

LD pruning with PLINK

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plink_ld_pruning(bfile, output.prefix, window.size, kb.window = FALSE,
  step.size, threshold, chr, ..., 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.
`window.size`	[`int`] Window size.
`kb.window`	[`boolean`] Is window size in kb units?
`step.size`	[`int`] Step size in variant counts.
`threshold`	[`number`] Pairwise r^2 threshold.
`chr`	[`number`] Restrict LD pruning to specified chromosome.
`...`	[`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.