dot-plink_fst: Internal Fst computation with PLINK

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

Description

Internal Fst computation with PLINK

Usage

.plink_fst(bed.file, bim.file, fam.file, output.prefix, pop.file, ...,
  exec, num.threads, memory)

Arguments

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.
output.prefix	[string] The basename of the output files.
pop.file	[string] File defining disjoint clusters/strata of samples. FIDs in the first column, IIDs in the second column, and cluster names in the third column.
...	[character] Additional arguments passed to PLINK call.
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.

Value

Captured system outputs as list of character vectors and number of samples excluded per criteria.

imbs-hl/imbs documentation built on Sept. 6, 2019, 11:05 p.m.