plink_ld_pruning: LD pruning with PLINK

Description Usage Arguments Details Value

View source: R/plink.R

Description

LD pruning with PLINK

Usage

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plink_ld_pruning(bfile, output.prefix, window.size, step.size, threshold, chr,
  ..., bed.file = NULL, bim.file = NULL, fam.file = NULL,
  exec = "plink", num.threads, memory)

Arguments

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 in kilobase.

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.

Details

See PLINK manual https://www.cog-genomics.org/plink/1.9/.

Value

Captured system output as character vector.


imbs-hl/imbs documentation built on Aug. 10, 2018, 3:56 a.m.