[BioC] Source code comments / read_abatch

Arkady bamboowarrior at gmail.com
Tue Jul 22 21:45:15 CEST 2008

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?

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.

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") ##
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'm guessing this is just me not understanding the code (usually the case).

Your help is greatly appreciated.

John Woods

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