plotvenn: Plots a venn digram to compare sample types Plots the number...

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

Description

Plots a venn digram to compare sample types Plots the number of type-specific and shared regulatory regions in a venn diagram Type of regulatroy region (enhancer, promoter, or both) and type of peak comparison (intensity or peak) must be specified.

Usage

plotvenn(analysisresultsmatrix, region = "both", method = "intensity",
  color = "redorange")

Arguments

analysisresultsmatrix	analysisresults of Intensity analysis place into analysisresults matrix by the analyzeanalysisresults function
region	pick a region, regions can be 'enhancer', 'promoter', or 'both' INCLUDE quotes
method	pick a method, methods can be 'intensity' or 'peak' include quotes
color	include the colors you want in your venn diagram

Value

venn diagram

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')
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)
analysisresults <- comparePeaksAltre(categaltre_peaks, reference= "SAEC")
plot1 <- plotvenn(analysisresults,
                  region='enhancer',
                  method='intensity')

## End(Not run)

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