[BioC] create CNA object in DNAcopy package with agilent data

[Sean Davis]

jhs1jjm at leeds.ac.uk wrote:
> Hi, I'm using R 2.5.0 on openSUSE 10.2 x86_64.
> 
> I'm struggling as to what to use for the chromosome and maploc arguments for the
> CNA function. I've got data from 3 agilent 44k CGH arrays. I've created the
> marrayNorm and Raw objects using read.Agilent. The CNA function usage is as
> follows:
> 
> CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"),
>                  sampleid=NULL)
> 
> I've read the CNA help page but am still struggling.
> For genomdat I've worked out this is mnorm at maM, the average log ratios, this
> will be my data.type.
> 
> The column headers in my raw data file include systematic name in the following
> format:
> 
> chr3:175483690-175483749
>
> This seems to have been read into my work session using read.Agilent but how do
> use this and it isn't ordered, is this important? I've looked at the coriell
> data example but this is all nicely ordered and the headers are different to my
> data file.
> 
> If anyone could point me in the right direction that would be great.

This is the information that you will need to use, yes.  It contains the
chromosome and location information.  You will need to manipulate this
column to get the chromosome and locations into separate columns.  You
can do this in R or in Excel.

Sean