plotAllelicCounts: plotAllelicCounts

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

Description

Creates an allelic counts plot, ie, counts of the alternative vs counts of the reference on the log10 scale. If significant and minor allele frequency columns present, dots will be highlighted accordingly.

Usage

plotAllelicCounts(
  data,
  title = NULL,
  padjCutoff = 0.05,
  allelicRatioCutoff = 0.8,
  rare_column = NULL
)

Arguments

data	A data.frame containing the counts or results table from DESeq4MAE function
title	The plot's title
padjCutoff	The significance level
allelicRatioCutoff	The minimum allelic ratio ALT/(ALT+REF) to be considered signficant
rare_column	The name of the column that indicates if a variant is rare or not. Default is null which means it won't be plotted.

Value

A ggplot object containing the MA plot.

Author(s)

Vicente Yepez

Examples

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

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