getBinAnnotations: Gets bin annotation data for a particular bin size

In QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

Description

Gets bin annotation data for a particular bin size.

Usage

getBinAnnotations(binSize, genome="hg19", type="SR50",
  path=getOption("QDNAseq::binAnnotationPath", NULL),
  verbose=getOption("QDNAseq::verbose", TRUE))

Arguments

binSize	A numeric scalar specifying the width of the bins in units of kbp (1000 base pairs), e.g. binSize=15 corresponds to 15 kbp bins.
genome	A character string specify the genome and genome version to be used.
type	A character string specify the experiment type, e.g. "SR50" or "PE100".
path	A character string specifying the path for the bin annotation file to be downloaded. The path can either be on the local file system or a URL online. If NULL (default), then data loaded from an R package named QDNAseq.{{genome}}. The default value can be controlled via R options QDNAseq::binAnnotationPath.
verbose	If TRUE, verbose messages are produced.

Details

Gets bin annotation data for a particular bin size.

Value

Returns a AnnotatedDataFrame object.

Author(s)

Ilari Scheinin

See Also

createBins().

Examples

## Not run: 
bins <- getBinAnnotations(15)

## End(Not run)

Example output

Loaded bin annotations for genome ‘hg19’, bin size 15 kbp, and experiment type ‘SR50’ from annotation package QDNAseq.hg19 v1.20.0

QDNAseq documentation built on Nov. 8, 2020, 6:57 p.m.