aggregateAlignment: Generate summaries on sliding windows over an alignment.

In gschofl/genoslideR: Create and manipulate multiple genome alignments with annotation.

Description

Generate summaries on sliding windows over an alignment.

Usage

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.