ReadPeaks reads in peak files and their cognate annotations created by findPeaks and annotatePeaks.pl. If input is super enhancer analysis, SuperEnhancerPlot takes in a the Normalized Tag Counts to produce a [0, 1] normalized plot with loading at enhancers. Combines super and typical enhancer peak data.tables and an optional gene list to annotate the plot.

SuperEnhancerPlot(se, te, gene.list = NULL, only.super.enhancers = TRUE)

Arguments

se

Super enhancer from HOMER findPeaks utility.

te

Typical enhancers from HOMER findPeaks utility; use -typical <filename> to produce analysis from findPeaks.

gene.list

character vector of gene ids (preferably Symbol); will find the best matches from Gene.Name and Gene.Alias annotation

only.super.enhancers

will only label super enhancers on gene.list (default: TRUE)

Value

ggplot2 of Super Enhancer Plot

Examples

super <- ReadPeaks(SE.peaks, SE.peaks.anno)
typical <- ReadPeaks(TE.peaks, TE.peaks.anno)
genes <- c("Tbx", "Fox") ## partial matching is OK
SuperEnhancerPlot(super, typical, genes)