GenomicAnnotations2reference_positions: extract reference positions from the GenomicAnnotations

Description Usage Arguments Value

Description

extract from the GenomicAnnotations object a vector containing a vector with reference positions

Usage

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# GenomicAnnotations2reference_positions(.Object,
# reference_position_type=c("start", "end", "median", "strand.start", "strand.end"),
# withnames=TRUE)

GenomicAnnotations2reference_positions(.Object, ...)

Arguments

.Object

Object of class GenomicAnnotations

...

See below

reference_position_type:

Specify which genomic coordinate must be used as reference position for PREDA analysis. Possible values are "start", "end", "median", "strand.start" or "strand.end".

"strand.start" is strand specific start: i.e. start on positive strand but end on negative strand. "strand.end" is strand specific end.

withnames:

Logical, if TRUE the "ids" slot content is used as names for the output vector

Value

A numeric vector with the selected reference positions.


PREDA documentation built on May 6, 2019, 2:07 a.m.