saasCNV (version 0.3.4)

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

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.

Value

An R plot will be generated.

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.

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)