Counts the number of sequencing reads surrounding supplied annotations

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Description

Counts are made in windows with boundaries fixed distances either side of a reference point.

Usage

# ANY,data.frame method
annotationCounts(x, anno, ...)
# ANY,GRanges method
annotationCounts(x, anno, up, down, ...)

Arguments

x:

A character vector of BAM paths, 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.

up:

The number of bases upstream to look.

down:

The number of bases downstream to look.

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 function called, but are passed into annotationBlocksCounts, that uses them in its processing.

Details

If the genomic features annotation contains all unstranded features, the up and down distances refer to how far towards the start of a chromosome, and how far towards the end to make the counting window boundaries. If the annotation is all stranded, then the up and down distances are relative to the TSS of the features.

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

annotationBlocksCounts, 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 = '+')

  annotationCounts(reads, genes, 500, 500, 300)

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