summarize.calls: Summarize genotype calls by sample or marker

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

Description

Summarize genotype calls by sample or marker

Usage

summarize.calls(gty, by = c("samples", "markers"), counts = TRUE, ...)

Arguments

gty	a genotypes object with intensity data attached
by	get call rates by sample or by marker
counts	logical; if TRUE, return absolute counts, otherwise relative frequencies
...	ignored

Details

Any metadata associated with markers or samples is *not* merged into the final result, in order to preserve parallelism between rows of the result and of the parent object.

Value

a dataframe with counts of A (reference or major allele), B (alternate or minor allele), H (heterozygous) and N (missing/no-call) by either sample or marker.

See Also

summarize.intensity, intensity.vs.ref, run.sample.qc

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