getBinAnnotations

A <code><a rd-options="base" href="/link/numeric?package=QDNAseq&version=1.8.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> scalar specifying the width of the bins
       in units of kbp (1000 base pairs), e.g. <code>binSize=15</code> corresponds
       to 15 kbp bins.

binSize

A <code><a rd-options="base" href="/link/character?package=QDNAseq&version=1.8.0&to=base" data-mini-rdoc="base::character">character</a></code> string specify the genome and genome version
       to be used.

genome

A <code><a rd-options="base" href="/link/character?package=QDNAseq&version=1.8.0&to=base" data-mini-rdoc="base::character">character</a></code> string specify the experiment type, e.g. "SR50"
       or "PE100".

type

A <code><a rd-options="base" href="/link/character?package=QDNAseq&version=1.8.0&to=base" data-mini-rdoc="base::character">character</a></code> string specifying the path for the bin
        annotation files. Defaults to downloading from the Internet, but can
        also be a local path. Can also be defined by setting the
        <code>QDNAseq::binAnnotationPath</code> option.

path


    Gets bin annotation data for a particular bin size.


Quantitative DNA sequencing for chromosomal aberrations.
The genome is divided into non-overlapping fixed-sized bins, number of
sequence reads in each counted, adjusted with a simultaneous
two-dimensional loess correction for sequence mappability and GC
content, and filtered to remove spurious regions in the genome.
Downstream steps of segmentation and calling are also implemented via
packages DNAcopy and CGHcall, respectively.

Daoud Sie

QDNAseq

Quantitative DNA sequencing for chromosomal aberrations

getBinAnnotations function

A <code><a href="numeric" rd-options="base">numeric</a></code> scalar specifying the width of the bins
       in units of kbp (1000 base pairs), e.g. <code>binSize=15</code> corresponds
       to 15 kbp bins.

A <code><a href="character" rd-options="base">character</a></code> string specify the genome and genome version
       to be used.

A <code><a href="character" rd-options="base">character</a></code> string specify the experiment type, e.g. "SR50"
       or "PE100".

A <code><a href="character" rd-options="base">character</a></code> string specifying the path for the bin
        annotation files. Defaults to downloading from the Internet, but can
        also be a local path. Can also be defined by setting the
        <code>QDNAseq::binAnnotationPath</code> option.

Gets bin annotation data for a particular bin size.

getBinAnnotations: Gets bin annotation data for a particular bin size

Description

Usage

Arguments

Value

Details

See Also

Examples