filter.plink: Filter markers and samples from a dataset with PLINK

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Filter markers and samples from a dataset with PLINK

Usage

filter.plink(prefix, out = NULL, chr = NULL, from = NULL, to = NULL,
  maf = 0, hwe = 1, geno.missing = 0, ind.missing = 0, attrib = NULL,
  attrib.file = NULL, remove = NULL, keep = NULL, remove.fam = NULL,
  keep.fam = NULL, flags = "", ...)

Arguments

prefix	a pointer to a PLINK fileset (of class plink)
out	filename prefix for filtered PLINK fileset; overrides prefix
chr	keep only markers on this chromosome
from	with chr, keep only markers with position greater than this
to	with chr, keep only markers with position less than this
maf	drop markers with minor-allele frequency lower than this threhsold
hwe	drop markers p-value less than this threshold for test of Hardy-Weinbery equilibrium
geno.missing	drop markers with call rate lower than this threshold
ind.missing	drop samples with call rate lower than this threshold
attrib	with attrib.file, keep only samples with these attribute(s) (labels)
attrib.file	with attrib, a file containing family IDs, sample IDs and attribute(s)
remove	character vector of samples to exclude
keep	character vector of samples to keep
remove.fam	character vector of family IDs to exclude
keep.fam	character vector of family IDs to keep
flags	additional command-line flags passed directly to PLINK call
...	ignored

Details

See the relevant PLINK documentation for details of the filters and precedence rules governing how they are applied.

Value

a pointer (of class plink) to a new PLINK binary fileset after application of the above filters

References

PLINK v1.9: https://www.cog-genomics.org/plink2

Purcell S et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3): 559-575. doi:10.1086/519795.

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.