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

In ewymathe/testALTREinstall: 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 enhancers/promoters
lfcshared	log2fold change cutoff (of chromatin accessibility) for shared enhancers/promoters
pvaltypespecific	p-value cutoff (of chromatin accessibility) for type specific enhancers/promoters
pvalshared	p-value cutoff (of chromatin accessibility) for shared enhancers/promoters

Value

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

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)
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
)

## End(Not run)

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