compare_ChIPseq_replicates: TF ChIPseq replicate correlation plots

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

This function generate the peak overlap statistics table for two TF ChIPseq replicates. Using common peaks, it plots the distribution and scatter plot of either -log10(p-value) or fold enrichment from peak file. Macs2 peak caller output files in narrowPeak/broadPeak format are used to extract the values.

Usage

compare_ChIPseq_replicates(
  sampleInfo,
  compare = "pvalue",
  yintercept = -Inf,
  summitRegion = 0,
  peakFormat
)

Arguments

sampleInfo	sample information dataframe
compare	One of pvalue or enrichment
yintercept	yintercept for horizontal line on beeswarm plot
summitRegion	Region width around peak summit to use for while merging the peaks from multiple samples. With increasing number of peaksets, the mearging of peaks creates broader consensus peaksets. Using a small region around peak summit allows to limit this consensus peak width. If 0 (default), whole peak region is used. If summitRegion > 0, 2 x summitRegion region around peak summit is used to create consensus peakset.
peakFormat	Format of the peak file. One of "narrowPeak", "broadPeak", "bed"

Value

A list with following ggplot2 elements:

• table: peak overlap summary table for replicates as a ggtable object

• distribution: Beeswarm plots showing comparative distribution between replicates for a metric of choice

• valueScatter: X-Y scatter plot using values a metric of choice

• rankScatter: X-Y scatter plot using rank(values) a metric of choice

Examples

NA

lakhanp1/chipmine documentation built on March 6, 2021, 9:06 a.m.