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

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

Description

Perform basic sample-wise QC on genotype calls and intensities

Usage

run.sample.qc(gty, ref.intensity = NULL, max.H = Inf, max.N = Inf,
  max.D = Inf, min.D = Inf, apply = FALSE, hits = 0, overwrite = TRUE,
  ...)

Arguments

gty	a genotypes object
ref.intensity	a vector of "sum-intensities" from known good reference samples
max.H	threshold for count of heterozygous calls, above which a sample is flagged; OR a named list of thresholds, with names to match "family ID" (column fid) in pedigree
max.N	threshold for count of no-calls, above which a sample is flagged; OR a named list as above
max.D	upper threshold for D-statistic (see intensity.vs.ref) above which a sample is flagged; OR a named list as above
min.D	lower threshold for D-statistic (see intensity.vs.ref) above which a sample is flagged; OR a named list as above
apply	logical; if TRUE, remove samples failing the filters, rather than flagging them
hits	samples failing more than this many filters are flagged
overwrite	logical; if TRUE (the default), replace exisitng filters with the results of this QC check
...	ignored

Details

A wrapper for the sample-level QC functions, applied to genotype calls (always) and hybridization intensities (if present.) Samplies which fail are flagged but not actually dropped from the result.

Value

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

See Also

summarize.calls, intensity.vs.ref, apply.filters

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