Creates a color-coded BED file for visualization of peaks and their ALTRE categories in a genome browser: red indicates increased log2fold change/low p-value, blue indicates decreased lod2fold change/low p-value, and purple indicates regions with little to no change and insignificant p-values. Based on the log2fold change and p-value inputs, there is a possibility that some regions will not fulfill any of the supplied criteria ("in-between" shared and type-specific). They are colored grey.
output generated from categAltrePeaks()
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## Not run: csvfile <- file.path(dir="yourfilepath", 'sampleinfo.csv') sampleinfo <- loadCSVFile(csvfile) samplePeaks <- loadBedFiles(sampleinfo) consPeaks <- getConsensusPeaks(samplepeaks=samplePeaks,minreps=2) TSSannot <- getTSS() consPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consPeaks, TSS = TSSannot, merge = TRUE, regionspecific = TRUE, distancefromTSSdist = 1500, distancefromTSSprox = 1000) #Need to run getcounts on all chromosomes counts_consPeaks <- getcounts(annotpeaks = consPeaksAnnotated, csvfile = csvfile, 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) writeBedFile(categaltre_peaks) ## End(Not run)
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