[BioC] DNACopy Question what is passed to the maploc argument.

[Valerie Obenchain]

Hi Nikolas,

Have your tried contacting the authors of DNAcopy? I've cc'd Venkatraman.

I don't have experience with this package but after reading Sean's 
response in the 2007 post and looking at CNA() my understanding is that 
'maploc' should be the start position of the target sequence. In your 
case, 175483690.

As an fyi, to see source code for any (non-generic) function just type 
the name. Sometimes useful if you have questions about how a variable is 
being handled ...

>> CNA
> function (genomdat, chrom, maploc, data.type = c("logratio",
>     "binary"), sampleid = NULL, presorted = FALSE)
> {
>     if (is.data.frame(genomdat))
>         genomdat <- as.matrix(genomdat)
>     if (!is.numeric(genomdat))
>         stop("genomdat must be numeric")
>     if (!is.numeric(maploc))
>         stop("maploc must be numeric")
...

Valerie



On 07/31/2014 08:12 AM, Nikolas Balanis wrote:
> Sorry to keep posting this, I am very new user of Bioconductor and I cant
> seem to find any clarification on this anywhere.. This is somewhat related
> to this question listed below, I just want some more clarification on using
> the CNA function. This is probably very elementary, I apologize in advance
>
> https://stat.ethz.ch/pipermail/bioconductor/2007-September/019138.html
>
>>From an agilent data set the SystematicName column is composed of elements
> of the form chr3:175483690-175485000. So for example for this element the
> chromosome # is 3, so the vector of these #s for all elements is passed as
> chrom in the CNA function. But what is the position numeric passed to
> maploc in the CNA function? From the documentation the maploc argument is
> "the locations of marker on the genome. Vector of length same as the number
> of rows of genomdat. This has to be numeric."  So it has to be numeric from
> the DNAcopy documentation. Is it the first value 175483690, the second
> value 175485000 , or the average of the two 175484345, or something else
> that I am missing completely? I
>
> 	[[alternative HTML version deleted]]
>
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-- 
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fhcrc.org
Phone: (206) 667-3158