zoomIntoRegion: Zoomed in view of genomic region

Description Usage Arguments Details Author(s) Examples

View source: R/zoomIntoRegion.R

Description

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

Usage

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  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 [email protected]

Examples

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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 May 2, 2018, 2:57 a.m.