getVariantPercentages: Variant coverage

In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System

Description

This function computes the coverage for each variant (in forward and/or reverse direction) for all samples. The coverage is defined as the percentual amount of reads that cover a variant.

Usage

getVariantPercentages(object, direction="both")

Arguments

object	An instance of class AVASet-class or MapperSet-class.
direction	A character indicating the direction ("forward", "reverse" or "both").

Details

If the direction was set to "both", the percentages are computed over the sum of both directions. Otherwise it is computed only over the occurences in one direction (forward or reverse). The occurences can be accesses via assayData.

Value

getVariantPercentages returns a data frame with all percentages/frequencies for all samples.

Author(s)

Christoph Bartenhagen

See Also

setVariantFilter.

Examples

# load a (filtered) AVA dataset containing 6 samples, 4 amplicons and 4 variants
data(avaSetFiltered)
avaSetFiltered

# both directions
getVariantPercentages(avaSetFiltered, direction="both")
# this is equivalent to
(assayData(avaSetFiltered)[[1]] + assayData(avaSetFiltered)[[3]]) / (assayData(avaSetFiltered)[[2]] + assayData(avaSetFiltered)[[4]])

# forward direction only
getVariantPercentages(avaSetFiltered, direction="forward")
# this is equivalent to
assayData(avaSetFiltered)[[1]] / assayData(avaSetFiltered)[[2]]

# reverse direction only
getVariantPercentages(avaSetFiltered, direction="reverse")
# this is equivalent to
assayData(avaSetFiltered)[[3]] / assayData(avaSetFiltered)[[4]]

R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.