Description Usage Arguments Examples
Plots venn diagrams for comparison of two methods of identifying altered regulatory regions Makes venn diagrams for enhancers, promoters, and combined for both intensity-based peaks and for peaks identified by hotspot calling algorithms. There is no return value. Six venn diagrams will be plotted
1 | plotallvenn(analysisresultsmatrix)
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analysisresultsmatrix |
analysisresults of countanalysis function place into a a analysisresults matrix by the analyzeanalysisresults function |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ## 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 <- resultsComparison(altre_peaks, reference= "SAEC")
plotallvenn(analysisresults)
## End(Not run)
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