I want to show the definition of readFastq. But showMethods doesn't show the function where I can find the body. Would you please let me know how to show the body of the function. > library(ShortRead) > showMethods('readFastq') Function: readFastq (package ShortRead) dirPath="SolexaPath" dirPath="character" -- Regards, Peng

On 05/22/2010 02:30 PM, Peng Yu wrote: > I want to show the definition of readFastq. But showMethods doesn't > show the function where I can find the body. Would you please let me > know how to show the body of the function. > >> library(ShortRead) >> showMethods('readFastq') > Function: readFastq (package ShortRead) > dirPath="SolexaPath" > dirPath="character" Hi Peng -- Use showMethods(readFastq, includeDef=TRUE) perhaps add class="character" or use selectMethod; later you might find it useful to remember ::: as a way to see unexported functions. Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

getMethods(mname) will retrieve definitions for all methods named mname getMethod(mname, sig) will retrieve definition for specified signature for your query > getMethod("readFastq", "character") Method Definition: function (dirPath, pattern = character(0), ...) { .local <- function (dirPath, pattern = character(0), ..., qualityType = c("Auto", "FastqQuality", "SFastqQuality"), filter = srFilter(), withIds = TRUE) { if (!missing(filter)) .check_type_and_length(filter, "SRFilter", NA) tryCatch(qualityType <- match.arg(qualityType), error = function(err) { .throw(SRError("UserArgumentMismatch", conditionMessage(err))) }) src <- .file_names(dirPath, pattern) elts <- .Call(.read_solexa_fastq, src, withIds) qualityFunc <- switch(qualityType, Auto = { alf <- alphabetFrequency(elts[["quality"]], collapse = TRUE) if (min(which(alf != 0)) < 59) FastqQuality else SFastqQuality }, SFastqQuality = SFastqQuality, FastqQuality = FastqQuality) quality <- qualityFunc(elts[["quality"]]) srq <- if (withIds) ShortReadQ(elts[["sread"]], quality, elts[["id"]]) else ShortReadQ(elts[["sread"]], quality) if (!missing(filter)) srq <- srq[filter(srq)] srq } .local(dirPath, pattern, ...) } <environment: namespace:shortread=""> Signatures: dirPath target "character" defined "character" it might be easier just to obtain the source version of the package and read as text On Sat, May 22, 2010 at 5:30 PM, Peng Yu <pengyu.ut@gmail.com> wrote: > I want to show the definition of readFastq. But showMethods doesn't > show the function where I can find the body. Would you please let me > know how to show the body of the function. > > > library(ShortRead) > > showMethods('readFastq') > Function: readFastq (package ShortRead) > dirPath="SolexaPath" > dirPath="character" > > > -- > Regards, > Peng > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]