comparePeaksAltre: Comparison of methods for identifying altered regulatory...

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

Description

Creates a table to compare two methods of identifying altered regulatory regions, one based on peak intensity, the other on peak presence as determined by hotspot calling algorithms.

Usage

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

Arguments

analysisresults	analysisresults of countanalysis.
lfctypespecific	log2fold change for type specific TSS-dists/TSS-proxs
lfcshared	log2fold chance for shared TSS-dists/TSS-proxs
pvaltypespecific	p-value for type specific TSS-dists/TSS-proxs
pvalshared	p-value for shared TSS-dists/TSS-proxs

Value

matrix comparing the two methods of identifying altered regulatory regions, one based on peak intensity, the other on peak presence as determined by hotspot calling algorithms.

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(alteredPeaks,
   lfctypespecific = 1.5,
   lfcshared = 1.2,
   pvaltypespecific = 0.01,
   pvalshared = 0.05)
comparePeaksAnalysisResults <- comparePeaksAltre(alteredPeaksCategorized)

## End(Not run)

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