refFrac: Reference allele fraction

In smgogarten/SeqVarTools: Tools for variant data

Reference allele fraction

Description

Calculate fraction of reference allele reads

Usage

## S4 method for signature 'SeqVarGDSClass'
refFrac(gdsobj, use.names=TRUE, parallel=FALSE)
## S4 method for signature 'SeqVarGDSClass'
refFracOverHets(gdsobj, FUN=mean, use.names=TRUE, parallel=FALSE)
## S4 method for signature 'SeqVarGDSClass'
refFracPlot(gdsobj, variant.id, highlight=NULL, ...)

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
FUN	The function to apply over heterozygote calls (mean or median).
use.names	A logical indicating whether to assign variant or samples IDs as names of the output vector.
parallel	Logical, numeric, or other value to control parallel processing; see seqParallel for details.
variant.id	A vector of variant.ids to plot.
highlight	A list of sample.ids to highlight with sequential integers on each plot
...	Additional arguments passed to plot.

Details

The variable "annotation/format/AD" (allelic depth) is required to compute the reference allele fraction.

refFracPlot generates plots of total unfiltered depth (sum over "AD" for all alleles) versus reference allele fraction. Points are color-coded by called genotype: teal = reference homozygote, orange = heterozygote including the reference allele, fuschia = heterozygote with two alternate alleles, purple = alternate homozygote, black = missing. Darker colors indicate a higher density of points. Vertical black line is at 0.5, vertical orange line is the median reference allele fraction for ref/alt heterozygotes. Values significantly different from 0.5 (after applying a Bonferroni correction) are plotted with triangles.

Value

refFrac returns a sample by variant array of the reference allele fraction, defined as ref_depth / total_depth.

refFracOverHets returns the mean (or other function, e.g. median) of reference allele depth (per variant) over all samples called as heterozygotes.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, applyMethod

Examples

gdsfile <- system.file("extdata", "hapmap_exome_chr22.gds", package="SeqVarTools")
gds <- seqOpen(gdsfile)
RF <- refFrac(gds)
dim(RF)
samples <- seqGetData(gds, "sample.id")
refFracPlot(gds, variant.id=5:6, 
            highlight=list(samples[2:3], samples[4:5]))
seqClose(gds)

smgogarten/SeqVarTools documentation built on Sept. 15, 2024, 1:08 p.m.