Creates a ‘copy number array’ data object used for DNA copy number
analyses by programs such as circular binary segmentation (CBS).
Usage
CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"),
sampleid=NULL, presorted = FALSE)
## S3 method for class 'CNA'
print(x, ...)
Arguments
genomdat
a vector or matrix of data from array-CGH, ROMA, or
other copy number experiments. If it is a matrix the rows correspond
to the markers and the columns to the samples.
chrom
the chromosomes (or other group identifier) from which
the markers came. Vector of length same as the number of rows of
genomdat. If one wants the chromosomes to be ordered in the
natural order, this variable should be numeric or ordered category.
maploc
the locations of marker on the genome. Vector of length
same as the number of rows of genomdat. This has to be numeric.
data.type
logratio (aCGH, ROMA, etc.) or binary (LOH).
sampleid
sample identifier. If missing the samples are named
by prefixing "Sample" to consecutive integers.
presorted
logical indicator telling if the data have already
been sorted by chrom and maploc. Default is FALSE.
x
object returned by CNA
...
arguments to be passed onto print command called within.
Details
Data that are NA, Inf, NaN will be removed on a per sample basis for
"genomdat" and all samples for "chrom" and "maploc".
If the chrom variable has non-numeric values make it into an ordered
variable to get them ordered correctly. E.g. for human genome use:
chrom <- ordered(chrom, levels=c(1:22,"X","Y")) to prepare the
variable if chromosomes X and Y are present in your data.
Value
An object of class CNA. There is a print method that
gives the number of samples and probes and the type of data.
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"))
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/CNA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CNA
> ### Title: Create 'Copy Number Array' data object
> ### Aliases: CNA print.CNA
> ### 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
>
>
>
>
>
>
> dev.off()
null device
1
>