[BioC] Source code comments / read_abatch

[James MacDonald]

This got taken off-list (please don't do that!). Here is the further 
exchange:

John O. Woods wrote:
 >> You wrote:
 >>
 >> If you want the comments, the easiest way is to download the package
 >> source and look at the files in the R directory.
 >>
 >
 > This is why this is such a trivial question.
 >
 > How do I download the package source? Naturally I could just go get 
  > the tarball, but is there an R command to do it?

LOL. This reminds me of a particular fortune:

 > fortune("Yoda")

Evelyn Hall: I would like to know how (if) I can extract some of the
information from the summary of my nlme.
Simon Blomberg: This is R. There is no if. Only how.
    -- Evelyn Hall and Simon 'Yoda' Blomberg
       R-help (April 2005)

So the answer is 'yes, of course'. You want:

setRepositories() #choose bioc software

then

download.packages("affy", ".", type = "source")

Best,

Jim


James W. MacDonald wrote:
> Arkady wrote:
>> This is probably a pretty trivial question.
>>
>> I know that if I type a function name in R, it'll print the function
>> for me. Unfortunately, it does so without comments. Is there a way to
>> get the function with comments?
> 
> If you want the comments, the easiest way is to download the package 
> source and look at the files in the R directory.
> 
>>
>> A related question: how can I access the documentation/comments for
>> internal .Call functions? I tried looking through my R libs dir, but
>> no luck.
> 
> These will be in the src directory of the package source.
> 
>>
>>
>> Particularly, I was wondering about this chunk of code in read.affybatch:
>>
>> headdetails <- .Call("ReadHeader", as.character(filenames[[1]]),
>> PACKAGE = "affyio")
>> dim.intensity <- headdetails[[2]]
>> ref.cdfName <- headdetails[[1]]
>> if (is.null(cdfname)) cdfname <- ref.cdfName
>> # ...
>> exprs <- .Call("read_abatch", filenames, rm.mask, rm.outliers,
>> rm.extra, ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio") ##
>> HERE #1
>> colnames(exprs) <- samplenames
>> if (!sd) {
>>   return(new("AffyBatch", exprs = exprs, cdfName = cdfname, phenoData
>> = phenoData, nrow = dim.intensity[1], ncol = dim.intensity[2],
>> annotation = cleancdfname(cdfname, addcdf = FALSE), description =
>> description, notes = notes)) ## HERE #2
>> }
>> else {
>> # ...
>> }
>>
>>
>> Shouldn't the line marked HERE #1 be using cdfname, NOT ref.cdfName?
>> The line marked HERE #2 uses cdfname as it (I think) should.
> 
> I don't think it matters at that point. All that is happening is the raw 
> data are being read into the AffyBatch object. If one is using a 
> non-standard cdf then it is when you compute expression values that it 
> is important to know what cdfenv to use, and as you note, the AffyBatch 
> gets the correct cdfname.
> 
> Best,
> 
> Jim
> 
> 
> 
>>
>> I'm guessing this is just me not understanding the code (usually the 
>> case).
>>
>> Your help is greatly appreciated.
>>
>>
>> Cheers,
>> John Woods
>>
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> 

-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623