Counts are made in windows with boundaries fixed distances either side of a reference point.
# ANY,data.frame method
annotationCounts(x, anno, ...)
# ANY,GRanges method
annotationCounts(x, anno, up, down, ...)
A character vector of BAM paths,
A set of genomic features to make windows around a reference point of
theirs. Either a
data.frame with (at least) colums
end, or a
The number of bases upstream to look.
The number of bases downstream to look.
If sequencing reads need to be extended, the fragment size to be used. Default: NULL (no extension).
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.
If the genomic features annotation contains all unstranded features, the
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
down distances are relative to the TSS of the features.
matrix of counts is returned, one column per sample and one row
per row of genomic features supplied.
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