enrichHeatmap: Given the output from enrichment(), creates a heatmap from...

In ewymathe/testALTREinstall: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

Given the output from enrichment(), creates a heatmap from the ouput of the enrichment analysis. Presence or absence of the pathway in enrichment of both type-specific (increased or decreased log2fold change, low p-value) and shared (no change, higher p-value) regulatory regions is plotted.

Usage

enrichHeatmap(input, title, pvalfilt = 0.01, removeonlyshared = FALSE,
  numshow = 10)

Arguments

input	results from enrichment analysis
title	title of the heatmap
pvalfilt	p-value cut-off for inclusion in heatmap
removeonlyshared	removes regions that come up signifigant only shared regulatory regions when set to TRUE. Default is FALSE.
numshow	number of top pathways (ranked according to p-value) of each type (expt, reference, shared) to show in the plot (default=10)

Value

heatmap

Examples

## Not run: 
dir <- system.file('extdata', package='ALTRE', mustWork=TRUE)
csvfile <- file.path(dir, 'lung.csv')
sampleinfo <- loadCSVFile(csvfile)
samplePeaks <- loadBedFiles(sampleinfo)
consPeaks <- getConsensusPeaks(samplepeaks = samplePeaks, minreps = 2)
plotConsensusPeaks(samplepeaks = consPeaks)
TSSannot <- getTSS()
consPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consPeaks,
                                          TSS = TSSannot,
                                          merge = TRUE,
                                          regionspecific = TRUE,
                                          mergedistenh = 1500,
                                          mergedistprom = 1000)
counts_consPeaks <- getCounts(annotpeaks = consPeaksAnnotated,
                              sampleinfo = sampleinfo,
                              reference = 'SAEC',
                              chrom = 'chr21')
altre_peaks <- countanalysis(counts=counts_consPeaks,
                             pval=0.01,
                             lfcvalue=1)
categaltre_peaks <- categAltrePeaks(altre_peaks,
			lfctypespecific = 1.5,
			lfcshared = 1.2,
			pvaltypespecific = 0.01,
			pvalshared = 0.05)
MFenrich <- pathenrich(analysisresults = categaltre_peaks,
                       ontoltype = 'MF',
                       enrichpvalfilt = 0.01)
BPenrich <- pathenrich(analysisresults=categaltre_peaks,
                       ontoltype='BP',
                       enrichpvalfilt=0.01)
plot1 <- enrichHeatmap(MFenrich, title='GO:MF, p<0.01')
plot2 <- enrichHeatmap(BPenrich, title='GO:BP, p<0.01')

## End(Not run)

ewymathe/testALTREinstall documentation built on May 16, 2019, 9:42 a.m.