Formatting code on blogger

http://stackoverflow.com/questions/679189/formatting-code-snippets-for-blogging-on-blogger



This one is using gist

Collection of resources explaining Bioconductor facilities

http://www.mas.ncl.ac.uk/~ncsg3/microarray/

Exploring S4 Objects in R

Looking what is inside of a particular method.
Method - spectra
Class - MSnExp
If method is exported (check NAMESPACE) then this will work.

getMethod("spectra","MSnExp")

Method Definition:
function (object) 
{
    sl <- as.list(assayData(object))
    fnames <- featureNames(object)
    return(sl[fnames])
}

Signatures:
        object  
target  "MSnExp"
defined "MSnExp"

Showing slots for a given class

showClass("MSnExp")

showMethods(classes="MSnExp", where="package:MSnbase")

The link to check http://missingreadme.wordpress.com/2011/01/04/how-to-see-the-code-for-s4-methods-in-r/

Debugging
trace(show, tracer=browser, signature=c(x="eSet"), where=getNamespace("Biobase"))

Where are the R libraries?

on Mac
/Library/Frameworks/R.framework/Versions/3.0/Resources/library
on Win
c:/Users/vlad/R/win-library/3.0