Tabulate insert sizes from paired-end alignments in bam files.

Read and tabulate the insert sizes from paired-end alignments contained in one or several bam files. By default, all properly aligned read pairs are included. Optionally, alignments can be restricted to those in a specific genomic region (regions argument) or the number of alignments read can be limited (nmax argument).

getInsertSizeDistFromBam(
  fname,
  regions = NULL,
  nmax = NA_integer_,
  isizemax = 800,
  exclude = c("chrM", "chrY", "chrX")
)

Arguments

fname

character vector with paths to one or several bam files. If multiple files are given, insert sizes from all will be pooled and tabulated together.

regions

GRanges object. Only alignments falling into these regions will be used. If NULL (the default), all alignments are used.

nmax

numeric(1) specifying the maximal number of alignments to read. If NA (the default), the alignments in regions (if regions are not NULL) or in the bam file will be used.

isizemax

numeric(1) specifying the maximal insert size to report. Larger insert sizes will be set to isizemax with on their number will be reported.

exclude

character vector with chromosome names to be excluded. Alignments on these chromosomes will be excluded. exclude will be ignored if regions is not NULL.

Value

integer vector with the number of insert sizes. The element at position i gives the observed number of alignment pairs with an insert size of i. The number of insert sizes greater than isizemax that were set to isizemax are reported in the attribute "ncapped".

See also

scanBam used to read alignments.

Author

Michael Stadler

Examples

if (requireNamespace("Rsamtools", quietly = TRUE)) {
    bamf <- system.file("extdata", "getInsertSizeDistFromBam", "atac_mm10.bam",
                        package = "swissknife")
    isize <- getInsertSizeDistFromBam(bamf)
    attr(isize, "ncapped")
    plot(isize, type = "l",
         xlab = "Insert size (bp)", ylab = "Number of fragments")
}