DESeq4MAE: Run deseq test for MAE

In mumichae/tMAE: Tests and visualizes for Mono-allelic expressed variants

Description

Uses a negative binomial test to determine if a variant is mono-allelically expressed.

Usage

DESeq4MAE(data, minCoverage = 10, disp = 0.05, independentFiltering = FALSE)

Arguments

data	A data.frame containing allelic counts.
minCoverage	minimum total allelic count. Default is 10.
disp	Gene dispersion for the NB test. Default is 0.05.
independentFiltering	Parameter that affects the multiple testing. Default is FALSE.

Value

Mono-allelic results table containing original counts plus p-value, p-adjusted and freqALT columns.

Author(s)

Vicente Yepez, Christian Mertes

Examples

file <- system.file("extdata", "allelic_counts_HG00187.csv", package = "tMAE", mustWork = TRUE)
maeCounts <- fread(file)
DESeq4MAE(maeCounts)

mumichae/tMAE documentation built on Oct. 11, 2021, 11:41 p.m.