plink_merge: Merge two PLINK datasets

In imbs-hl/imbs: Collection of functions used at the IMBS

Description

Merge two PLINK datasets

Usage

plink_merge(first.prefix, second.prefix, merge.mode, output.prefix, ...,
  first.bed.file = NULL, first.bim.file = NULL,
  first.fam.file = NULL, second.bed.file = NULL,
  second.bim.file = NULL, second.fam.file = NULL, exec = "plink2",
  num.threads, memory)

Arguments

first.prefix	[string] The basename of the first binary PLINK file set.
second.prefix	[string] The basename of the second binary PLINK file set.
merge.mode	[int] Merge mode.
output.prefix	[string] The basename of the output binary PLINK file set.
...	[character] Additional arguments passed to PLINK.
first.bed.file	[string] Alternative to bfile interface. Specify bed, bim and fam files individually.
first.bim.file	[string] Alternative to bfile interface. Specify bed, bim and fam files individually.
first.fam.file	[string] Alternative to bfile interface. Specify bed, bim and fam files individually.
second.bed.file	[string] Alternative to bfile interface. Specify bed, bim and fam files individually.
second.bim.file	[string] Alternative to bfile interface. Specify bed, bim and fam files individually.
second.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 Sept. 6, 2019, 11:05 p.m.