PlotChIPHeatmaps: Plot ChIP heatmaps

In j-andrews7/OneLinerOmics: One-liner RNA-seq and ChIP-seq Analyses

Description

PlotChIPHetmaps generates signal and correlation heatmaps for a DBA object.

Usage

PlotChIPHeatmaps(
  results,
  outpath,
  method,
  breaks,
  colors,
  fdr.thresh = 1,
  fc.thresh = 0,
  consensus = TRUE
)

Arguments

results	DBA object as returned by dba.analyze.
outpath	Path to directory to be used for output.
method	Method used for DiffBind analyses (e.g. DBA_DESEQ2).
breaks	Scalar vector of breaks to use for color mapping.
colors	Vectors of colors to use for color mapping.
fdr.thresh	Number indicating FDR threshold. Peaks greater than fdr.thresh will not be included in the heatmap or used for sample correlations.
fc.thresh	Number indicating absolute log fold-change that peaks must meet to be included in the heatmaps or used for sample correlations.
consensus	Boolean indicating whether creating heatmaps for consensus peaks.

Details

This function will generate heatmaps for each contrast individually as well as all differentially bound peaks in all samples if consensus = FALSE. A table will be saved of all peaks in the combined heatmap, with row order retained if row clustering is performed.

Author(s)

Jared Andrews

j-andrews7/OneLinerOmics documentation built on Sept. 9, 2021, 11 a.m.