plink_rm_high_ld: Remove regions of high LD
In imbs-hl/imbs: Collection of functions used at the IMBS

Description Usage Arguments Details Value

There are regions of long-range, high linkage diequilibrium in the human genome. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

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plink_rm_high_ld(bfile, output.prefix, build = "b37", ...,
  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.
`build`	[`integer`] The genome build version of PLINK file. Default b37.
`...`	[`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_NODE` and `num.threads * SLURM_MEM_PER_CPU` and at least 5000.