getCounts: getCounts

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

getCounts

Description

Creates a SummarizedExperiment of fragment (or insertion) counts from bam files that overlap given regions.

Usage

getCounts(
  bam_files,
  regions,
  paired,
  extend = 0L,
  shift = 0L,
  type = c("full", "center", "start", "end", "ends"),
  ov.type = "any",
  maxgap = -1L,
  minoverlap = 1L,
  ignore.strand = TRUE,
  strandMode = 1,
  includeDuplicates = TRUE,
  includeSecondary = FALSE,
  minMapq = 1L,
  minFragLength = 1L,
  maxFragLength = 5000L,
  splitByChr = 3,
  randomAcc = FALSE,
  verbose = TRUE
)

Arguments

bam_files	A vector of paths to the bam files.
regions	A 'GRanges' of regions in which to counts.
paired	Logical; whether the data is paired (assumed unpaired by default). Use 'paired="auto"' for automatic detection using the first bam file.
extend	The amount *by* which to extend single-end reads (e.g. fragment length minus read length). If 'paired=TRUE' and 'type' is either 'ends' or 'center', then the extension will be applied after taking the (shifted) fragment ends or centers, resulting in ranges of width equal to 'extend'.
shift	Shift (from 3' to 5') by which reads/fragments will be shifted. If 'shift' is an integer vector of length 2, the first value will represent the shift for the positive strand, and the second for the negative strand. For ATACseq data, one normally uses 'shift=c(4L,-5L)'.
type	Type of the coverage to compile. Either full (full read/fragment), start (count read/fragment start locations), end, center, or 'ends' (both ends of the read/fragment).
ov.type	Overlap type. See the 'type' argument of link[GenomicRanges]{countOverlaps}.
maxgap	Maximum gap allowed for overlaps (see the corresponding argument of link[GenomicRanges]{countOverlaps}).
minoverlap	Minimum overlap (see the corresponding argument of link[GenomicRanges]{countOverlaps}).
ignore.strand	Logical; whether to ignore strand for the purpose of counting overlaps (default TRUE).
strandMode	The strandMode of the data (whether the strand is given by the first or second mate, which depends on the library prep protocol). See strandMode for more information. This parameter has no effect unless one of the 'strand', 'extend' parameters or a strand-specific 'shift' are used.
includeDuplicates	Logical, whether to include reads flagged as duplicates.
includeSecondary	Logical; whether to include secondary alignments
minMapq	Minimum mapping quality (1 to 255)
minFragLength	Minimum fragment length (ignored if 'paired=FALSE')
maxFragLength	Maximum fragment length (ignored if 'paired=FALSE')
splitByChr	Whether to process chromosomes separately, and if so by how many chunks. The should not affect the output, and is simply slightly slower and consumes less memory. Can be a logical value (in which case each chromosome is processed separately), but we instead recommend giving a positive integer indicating the number of chunks.
randomAcc	Logical, whether to use random access. This is disabled by default because the overhead of random access to a lot of regions is typically worse than reading the entire file. However, if you need to get counts in few regions, enabling this will be faster. Note however that when using random access, the output object will not contain depth information.
verbose	Logical; whether to print progress messages

Value

A RangedSummarizedExperiment with a 'counts' assay.

Examples

# get an example bam file
bam <- system.file("extdata", "ex1.bam", package="Rsamtools")
# create regions of interest
peaks <- GRanges(c("seq1","seq1","seq2"), IRanges(c(400,900,500), width=100))
getCounts(bam, peaks, paired=FALSE)

ETHZ-INS/epiwraps documentation built on Dec. 22, 2024, 4:05 a.m.