gene.coverage.hist: Plots the gene coverage for a given gene

In helen-zhu/ConsensusPeaks: A Method for Peak Merging And Distribution Fitting Across Biological Replicates

Description

Plots the gene coverage for a given gene

Usage

gene.coverage.hist(PEAKS, GENE, ANNOTATION)

Arguments

PEAKS	A data frame containing the following columns, and potentially extras, usually found in a BED12 file, base 0 system
ANNOTATION	Annotations returned from read.gtf.
GENES	A character vector of genes to be tested

Value

ggplot of the gene coverage histogram

Examples

gtf.path = system.file("extdata/test.gtf", package = "ConsensusPeaks")
PARAMETERS = list("GTF" = gtf, "GENE" = "ENSGXX")
annotation = read.gtf(PARAMETERS)
ensgxx = simulate.gaussian.peaks(
  MU = c(100, 150),
  SD = c(10, 20),
  EXTEND.WIDTH = c(50, 25),
  NSAMPLES = c(10, 30),
  GENE = "ENSGXX",
  GTF = gtf,
  ANNOTATION = annotation,
  SEED = 123)
gene.coverage.hist(ensgxx, "ENSGXX", annotation)

helen-zhu/ConsensusPeaks documentation built on Dec. 25, 2021, 9:39 a.m.