zoomIntoRegion: Zoomed in view of genomic region

In DNAcopy: DNA copy number data analysis

Description

This program computes the frequency of gains and losses for each probe as a function of level of mad.

Usage

  zoomIntoRegion(x, chrom, sampleid, maploc.start=NULL, maploc.end=NULL,
      pt.pch=NULL, pt.cex=NULL, pt.col=NULL, segcol=NULL, seglwd=NULL,
      main=NULL, xlab=NULL, ylab=NULL, ...)

Arguments

x	an object of class DNAcopy.
chrom	the chromosome in which the region lies.
sampleid	the sample of interest.
maploc.start	genomic start position of the region of interest. Default is the beginning of the chromosome.
maploc.end	genomic end position of the region of interest. Default is the end of the chromosome.
pt.pch	the plotting character used for plotting the log-ratio values (default is ".").
pt.cex	the size of plotting character used for the log-ratio values (default is 3 if "." and 1 otherwise).
pt.col	the color used for the points. Default is green3.
segcol	the color of the lines indicating the segment means. If missing the line color is set to be red.
seglwd	line weight of lines for segment mean and zeroline. If missing it is set to 3.
main	figure title. If missing will be generated by pasting the chromosome, range and sample name together.
xlab	x-axis label. If missing "Genomic position" will be used
ylab	y-axis label. If missing "log-ratio" will be used
...	additional plotting options.

Details

This command plots the region of interest with the log-ratio and segments. It works for a region from a single chromosome in a single sample. So if more than one chromosome and/or one sample are given only the first chromosome from the first sample will be used.

Author(s)

Venkatraman E. Seshan [e-mail]

Examples

data(coriell)

#Combine into one CNA object to prepare for analysis on Chromosomes 1-23

CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330),
                  coriell$Chromosome,coriell$Position,
                  data.type="logratio",sampleid=c("c05296","c13330"))

#We generally recommend smoothing single point outliers before analysis
#Make sure to check that the smoothing is proper

smoothed.CNA.object <- smooth.CNA(CNA.object)

#Segmentation at default parameters

segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose=1)

zoomIntoRegion(segment.smoothed.CNA.object, chrom=10, sampleid="c05296")

Example output

Warning message:
In CNA(cbind(coriell$Coriell.05296, coriell$Coriell.13330), coriell$Chromosome,  :
  array has repeated maploc positions

Analyzing: c05296 
Analyzing: c13330 

DNAcopy documentation built on Nov. 8, 2020, 5:48 p.m.