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

[SeshanV at mskcc.org]

Hi Nikolas,

Here is what the help for CNA says:

   maploc: the locations of marker on the genome.  Vector of length same
           as the number of rows of genomdat. This has to be numeric.

That is, it is the genomic position at which the copy number information
is being measured.

In the link that you provided the probe on the array being referred to is
chr3:175483690-175483749. Thus it measures the copy number information in
a small interval encompassing the probe. However, as Valerie pointed out,
maploc is a numeric variable used to represent this interval. Thus any
value in the interval is valid for maploc as long as two different
(overlapping) probes do not get the same position to represent it.


Venkat

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Director of Biostatistics Computer-Intensive Support Services
Department of Epidemiology and Biostatistics | MSKCC
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On 7/31/14 12:54 PM, "Valerie Obenchain" <vobencha at fhcrc.org> wrote:

>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
>


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