PlotChIPPCAs: Plot ChIP PCAs

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

Description

PlotChIPPCAs generates PCA plots for all contrasts found in results. If consensus = TRUE, it will also generate one with all samples and all peaks.

Usage

PlotChIPPCAs(
  results,
  outpath,
  method,
  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).
fdr.thresh	Number indicating FDR threshold. Peaks greater than fdr.thresh will not be used for PCAs.
fc.thresh	Number indicating absolute log fold-change that peaks must meet to be used for the PCA.
consensus	Boolean indicating whether PCAs are for consensus peaks.

Author(s)

Jared Andrews

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