getCounts: Generates count data for regulatory regions. This function is...

In Mathelab/ALTRE: 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. The function getCounts generates count data using the summerizeOverlaps function from the GenomicAlignments package. This function is slower than the count function getCountsFast in the ALTRE package. However, getCounts MUST be used to count reads on a Windows computer – getCountsFast is not available in Windows. If the package is being run on Linux or MacOS, use getCountsFast. For high-thoughput experiments (many samples need to be analyzed), it is highly suggested that a non-Windows computer is used (MacOS/Linux). To be clear: GetCounts and getCountsFast give the EXACT SAME results.

Usage

getCounts(annotpeaks, sampleinfo, reference, singleEnd = TRUE, 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
singleEnd	whether input data is single-end (default is TRUE)
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 TSS-distal and TSS-proximal before and after filtering (if applicable) (3) Data frame for creating a density plot (use function plotgetcounts()

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')

## End(Not run)

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