aggregateAlignment: Generate summaries on sliding windows over an alignment.

Description Usage Arguments Details Value

View source: R/aggregate-alignment.R

Description

Generate summaries on sliding windows over an alignment.

Usage

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aggregateAlignment(aln, ranges = NULL, window = NULL, step = NULL,
  f = "Eta", ...)

Arguments

aln

An annotatedAlignment or DNAStringSet object.

ranges

A GRanges object holding genomic windows on which summaries are generated.

window

Sliding window size. If no ranges are specified sliding windows are constructed over the complete alignment, otherwise sliding windows are constructed within each genomic window specified by ranges.

step

Step size of sliding windows.

f

Function applied to each window of aln.

...

Further arguments for f.

Details

The function f applied to each window must accept a DNAStringSet as input and generate a named vector as output.

Value

A RangedDataList.


gschofl/genoslideR documentation built on May 17, 2019, 8:52 a.m.