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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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