varqual2summary: Summary per variant

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Summary per variant

Description

Compute the mean, sd, min, Q1, med, mean, Q3, max of the genotype qualities per variant, also reporting the number of samples and the number of missing data.

Usage

varqual2summary(vcf, fields = "GQ")

Arguments

vcf	CollapsedVCF (see pkg VariantAnnotation)
fields	genotype field(s) of the VCF to parse ("DP"/"GQ"/c("DP","GQ"))

Value

list of matrices (one per field) with one row per variant and 9 columns (n, na, mean, sd, min, q1, med, q3, max)

Author(s)

Timothee Flutre

See Also

summaryVariant

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.