[BioC] Source code comments / read_abatch

[James W. MacDonald]

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, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662