compHOMER: Function to compare two sets of HOMER known motif enrichment...

In kevincjnixon/ChIPATAC: Wrapper functions for useful genomic analyses like ChIP-seq or ATAC-seq.

Function to compare two sets of HOMER known motif enrichment results Results from HOMER known TF motif enrichment analyses are ranked either by enrichment or significance and plotted for comparison

Description

Function to compare two sets of HOMER known motif enrichment results Results from HOMER known TF motif enrichment analyses are ranked either by enrichment or significance and plotted for comparison

Usage

compHOMER(
  xfile,
  yfile,
  title = "",
  xlab = "x",
  ylab = "y",
  lab = T,
  spec = NULL,
  numLab = 5,
  enrichment = F,
  returnRes = F
)

Arguments

xfile	string of path to knownResults.txt file of a HOMER motif enrichment analysis
yfile	string of path to knownResults.txt file of another HOMER motif enrichment analysis
title	String indicating title of figure
xlab	String indicating the x-axis label (describing xfile). Default="x"
ylab	String indicating the y-axis label (describing yfile). Default="y"
lab	Boolean indicating if certain TFs should be labeled
spec	String vector indicating TFs of interest that should be labeled
numLab	Numeric indicating the number of top ranked TFs to be labeled (default=5)
enrichment	Boolean indicating if the results should be ranked by enrichment. FALSE ranks results by significance. Default=FALSE.
returnRes	Boolean indicating if data frame of results should be returned. Default=F.
return	Plot comparing HOMER results. Data frame of TFs and corresponding rankings and differences between those rankings.

kevincjnixon/ChIPATAC documentation built on May 25, 2023, 9:33 p.m.