genome.wide.plot: Visualize Genome-Wide SCNA Profile

In saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

Description

An optional function to visualize genome-wide SCNA Profile.

Usage

genome.wide.plot(data, segs, sample.id, chrs, cex = 0.3)

Arguments

data	a data frame containing log2ratio and log2mBAF data generated by cnv.data.
segs	a data frame containing segment location, summary statistics and SCNA status resulting from cnv.call.
sample.id	sample ID to be displayed in the title of the plot.
chrs	the chromosomes to be visualized. For example, 1:22.
cex	a numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. It can be adjusted in order to make the plot legible.

Details

On the top panel, the log2ratio signal is plotted against chromosomal position and on the panels blow, the log2mBAF, tumor mBAF, and normal mBAF signals. The dots, each representing a probe data point, are colored alternately to distinguish chromosomes. The segments, each representing a DNA segment resulting from the joint segmentation, are colored based on inferred copy number status.

Value

An R plot will be generated.

Author(s)

Zhongyang Zhang <[e-mail]>

See Also

joint.segmentation, cnv.call, diagnosis.seg.plot.chr, diagnosis.cluster.plot

Examples

data(seq.data)
data(seq.cnv)

genome.wide.plot(data=seq.data, segs=seq.cnv, 
                 sample.id="PT116", 
                 chrs=sub("^chr","",unique(seq.cnv$chr)), 
                 cex=0.3)

Example output

Loading required package: RANN
Loading required package: DNAcopy

saasCNV documentation built on May 1, 2019, 7:49 p.m.