getCounts {chromVAR} | R Documentation

## getCounts

### Description

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

### Usage

    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

    # 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")

[Package chromVAR version 1.4.1 Index]