getCounts

makes matrix of fragment counts in peaks using one or multiple bam or bed files

getCounts(alignment_files, peaks, paired, by_rg = FALSE, format = c("bam",
  "bed"), colData = NULL)

Arguments

alignment_files	filenames for bam or bed files with aligned reads
peaks	GRanges object with peaks
paired	paired end data?
by_rg	use RG tags in bam to separate groups?
format	bam or bed? default is bam
colData	sample annotation DataFrame

Value

RangedSummarizedExperiment-class object

See also

getSampleDepths, getPeaks, filterSamples

Examples

# NOT RUN {
# First we'll read in some peaks
peaks_file <- system.file("extdata", "test_bed.txt", package = "chromVAR")
test_peaks <- getPeaks(peaks_file, sort = TRUE)

# With single bam with RG tags (can also give multiple bams with RG)
test_rg <- system.file("extdata", "test_RG.bam", package = "chromVAR")
test_counts <- getCounts(test_rg, peaks = test_peaks, by_rg = TRUE,
                          paired = TRUE,
                          colData = S4Vectors::DataFrame(condition ="A"))


# Multiple bams without RG tags
test_bam1 <- system.file("extdata", "test_single1.bam", package = "chromVAR")
test_bam2 <- system.file("extdata", "test_single2.bam", package = "chromVAR")
test_bam3 <- system.file("extdata", "test_single3.bam", package = "chromVAR")
test_counts2 <- getCounts(c(test_bam1, test_bam2,test_bam3),
                           peaks = test_peaks, by_rg = FALSE,
                           paired = TRUE,
                           colData = S4Vectors::DataFrame(celltype =
                                                          c("A","B","C")))

# Bed file with reads (can give multiple bed files, here we will just read 1)
test_bed <- system.file("extdata", "test_reads.bed", package = "chromVAR")
test_counts3 <- getCounts(test_bed, test_peaks, by_rg = FALSE,
                           paired = FALSE,
                           format = "bed")
# }