categAltrePeaks: Categorize altered peaks as experiment-specific,...

In Mathelab/ALTRE: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

Categorize altered peaks as experiment-specific, reference-specific, or shared

Usage

categAltrePeaks(analysisresults, lfctypespecific = 1.5, lfcshared = 1.2,
  pvaltypespecific = 0.01, pvalshared = 0.05)

Arguments

analysisresults	output of countanalysis()
lfctypespecific	log2fold change cutoff (of chromatin accessibility) for type specific TSS-distals/TSS-proximals
lfcshared	log2fold change cutoff (of chromatin accessibility) for shared TSS-distals/TSS-proximals
pvaltypespecific	p-value cutoff (of chromatin accessibility) for type specific TSS-distals/TSS-proximals
pvalshared	p-value cutoff (of chromatin accessibility) for shared TSS-distals/TSS-proximals

Value

list 1) results of countanalysis, 2) Frequences of sample type specific, shared, and ambiguous regulatory elements

Examples

## Not run: 
csvfile <- loadCSVFile("DNaseEncodeExample.csv")
samplePeaks <- loadBedFiles(csvfile)
consensusPeaks <- getConsensusPeaks(samplepeaks = samplePeaks, minreps = 2)
TSSannot <- getTSS()
consensusPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consensusPeaks,
   TSS = TSSannot,
   merge = TRUE,
   regionspecific = TRUE,
   distancefromTSSdist = 1500,
   distancefromTSSprox = 1000)
consensusPeaksCounts <- getCounts(annotpeaks = consensusPeaksAnnotated,
   sampleinfo = csvfile,
   reference = 'SAEC',
   chrom = 'chr21')
alteredPeaks <- countanalysis(counts = consensusPeaksCounts,
   pval = 0.01,
   lfcvalue = 1)
alteredPeaksCategorized <- categAltrePeaks(analysisresults = alteredPeaks,
   lfctypespecific = 1.5,
   lfcshared = 1.2,
   pvaltypespecific = 0.01,
   pvalshared = 0.05)

## End(Not run)

Mathelab/ALTRE documentation built on May 7, 2019, 3:41 p.m.