getCounts: Generates count data for regulatory regions

In ewymathe/testALTREinstall: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

Counts the number of reads in each regulatory region for each sample type – read count is derived from user-input BAM filex, and regions of interest are supplied in a Granges object, ideally output of combineannotatepeaks.R.

Usage

getCounts(annotpeaks, sampleinfo, reference, chrom = NULL)

Arguments

annotpeaks	list output from combineannotatepeaks function
sampleinfo	dataframe as returned from loadCSVFile() function
reference	name of sample type to be considered 'reference' in DESeq2 analysis
chrom	optional, only chromosome chrom will be evaluated

Value

List containing three items: (1) DESeqDataSet: contains count information for all replicates of all samples (2) Matrix: contains number of enhancers and promoters before and after filtering (if applicable) (3) Data frame for creating a density plot (use function plotgetcounts()

Examples

## Not run: 
TSSannot <- getTSS()
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)
consPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consPeaks,
                                          TSS = TSSannot,
                                          merge = TRUE,
                                          regionspecific = TRUE,
                                          mergedistenh = 1500,
                                          mergedistprom = 1000 )
counts_consPeaks <- getCounts(annotpeaks = consPeaksAnnotated,
                              sampleinfo = sampleinfo,
                              reference = 'SAEC',
                              chrom = 'chr21')

## End(Not run)

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