zoomIntoRegion {DNAcopy} | R Documentation |
This program computes the frequency of gains and losses for each probe as a function of level of mad.
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, ...)
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. |
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.
Venkatraman E. Seshan seshanv@mskcc.org
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")