diagnosis.cluster.plot: Visualize Genome-Wide SCNA Profile in 2D Cluster Plot

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

Description

An optional function to visualize genome-wide SCNA Profile in log2mBAF-log2ratio 2D cluster plot.

Usage

diagnosis.cluster.plot(segs, chrs, min.snps, max.cex = 3, ref.num.probe = NULL)

Arguments

segs	a data frame containing segment location, summary statistics and SCNA status resulting from cnv.call.
chrs	the chromosomes to be visualized. For example, 1:22.
min.snps	the minimum number of probes a segment span.
max.cex	the maximum of cex a circle is associated with. See details.
ref.num.probe	integer. The reference number of probes against which a segment is compared in order to determine the cex of the segment to be displayed. Default is NULL. If NULL, It will be automatically specified as 1/100 of the number of data points.

Details

on the main log2mBAF-log2ratio panel, each circle corresponds to a segment, with the size reflecting the length of the segment; the color code is specified in legend; the dashed gray lines indicate the adjusted baselines. The side panels, corresponding to log2ratio and log2mBAF dimension respectively, show the distribution of median values of each segment weighted by its length.

Value

An R plot will be generated.

Author(s)

Zhongyang Zhang <[e-mail]>

See Also

joint.segmentation, cnv.call, diagnosis.seg.plot.chr, genome.wide.plot

Examples

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

diagnosis.cluster.plot(segs=seq.cnv, 
                       chrs=sub("^chr","",unique(seq.cnv$chr)), 
                       min.snps=10, max.cex=3, ref.num.probe=1000)

Example output

Loading required package: RANN
Loading required package: DNAcopy

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