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.
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")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(DNAcopy)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DNAcopy/zoomIntoRegion.Rd_%03d_medium.png", width=480, height=480)
> ### Name: zoomIntoRegion
> ### Title: Zoomed in view of genomic region
> ### Aliases: zoomIntoRegion
> ### Keywords: nonparametric
>
> ### ** 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"))
Warning message:
In CNA(cbind(coriell$Coriell.05296, coriell$Coriell.13330), coriell$Chromosome, :
array has repeated maploc positions
>
> #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)
Analyzing: c05296
Analyzing: c13330
>
> zoomIntoRegion(segment.smoothed.CNA.object, chrom=10, sampleid="c05296")
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.