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

In ewymathe/testALTREinstall: 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, reference, lfctypespecific = 1.5,
  lfcshared = 1.2, pvaltypespecific = 0.01, pvalshared = 0.05)

Arguments

analysisresults	analysisresults of countanalysis.
reference	cell type to be considered "reference" or "reference" to which other cell types will be compared
lfctypespecific	log2fold change for type specific enhancers/promoters
lfcshared	log2fold chance for shared enhancers/promoters
pvaltypespecific	p-value for type specific enhancers/promoters
pvalshared	p-value for shared enhancers/promoters

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: 
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')

## End(Not run)

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