run.marker.qc: Perform basic marker-wise QC on genotype calls

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

Description

Perform basic marker-wise QC on genotype calls

Usage

run.marker.qc(gty, max.H = Inf, max.N = Inf, min.hom = 0, hits = 0,
  apply = FALSE, overwrite = TRUE, ...)

Arguments

gty	a genotypes object
max.H	threshold for count of heterozygous calls, above which a site is flagged
max.N	threshold for count of no-calls, above which a site is flagged
min.hom	threshold for count of homozygous calls, at or below which a site is flagged
hits	markers failing more than this many filters are flagged
apply	logical; if TRUE, remove markers failing the filters, rather than flagging them
overwrite	logical; if TRUE (the default), replace exisitng filters with the results of this QC check
...	ignored

Details

A wrapper for the marker-level QC functions, applied to genotype calls. Samplies which fail are flagged but not actually dropped from the result (unless apply = TRUE.)

Value

a copy of the input with sample filters set, and an object of class marker.QC.result in attr(,"marker.qc")

See Also

summarize.calls, run.sample.qc, apply.filters

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