Counts the number of sequencing reads within supplied genomic blocks.

Description

Counts reads inside blocks.

Usage

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  ## S4 method for signature 'ANY,data.frame'
annotationBlocksCounts(x, anno, ...)
  ## S4 method for signature 'character,GRanges'
annotationBlocksCounts(x, anno, ...)
  ## S4 method for signature 'GRanges,GRanges'
annotationBlocksCounts(x, anno, seq.len = NULL, verbose = TRUE)
  ## S4 method for signature 'GRangesList,GRanges'
annotationBlocksCounts(x, anno, ...)

Arguments

x

A character vector of BAM paths, a GRangesList, or GRanges object.

anno

A set of genomic features to make windows around a reference point of theirs. Either a data.frame with (at least) colums chr, start, and end, or a GRanges object.

seq.len

If sequencing reads need to be extended, the fragment size to be used. Default: NULL (no extension).

verbose

Whether to print progress. Default: TRUE.

...

Parameters described above, that are not used in the top-level error-checking stage, but are passed further into a private function that uses them in its processing.

Value

A matrix of counts is returned, one column per sample and one row per row of genomic features supplied.

Author(s)

Aaron Statham

See Also

annotationCounts, genomeBlocks

Examples

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  require(GenomicRanges)
  reads <- GRanges(seqnames = rep("chr1", 5),
                   IRanges(c(3309, 4756, 4801, 4804, 5392), width = 36),
                   strand = c('+', '-', '-', '+', '+'))
  genes <- GRanges("chr1", IRanges(5000, 7000), strand = '+')
  annotationBlocksCounts(reads, genes, 300)

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