How to show the definition of readFastq
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Peng Yu ▴ 940
@peng-yu-3586
Last seen 9.6 years ago
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
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@martin-morgan-1513
Last seen 3 days ago
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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
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@vincent-j-carey-jr-4
Last seen 5 weeks ago
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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]]
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On Sat, May 22, 2010 at 4:40 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > 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") Why the following command doesn't work for 'quality'? > getMethod('quality', 'ShortReadQ') Error in getMethod("quality", "ShortReadQ") : No method found for function "quality" and signature ShortReadQ > showMethods('quality') Function: quality (package Biostrings) x="ANY" x="FastqQuality" (inherited from: x="ANY") x="ShortReadQ" (inherited from: x="ANY") -- Regards, Peng
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On 05/22/2010 03:46 PM, Peng Yu wrote: > On Sat, May 22, 2010 at 4:40 PM, Vincent Carey > <stvjc at="" channing.harvard.edu=""> wrote: >> 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") > > Why the following command doesn't work for 'quality'? > >> getMethod('quality', 'ShortReadQ') > Error in getMethod("quality", "ShortReadQ") : No method found for > function "quality" and signature ShortReadQ >> showMethods('quality') > Function: quality (package Biostrings) x="ANY" x="FastqQuality" > (inherited from: x="ANY") x="ShortReadQ" (inherited from: x="ANY") see ?getMethod and the difference between selectMethod and getMethod, conveniently documented on the same page. A call to ?getMethod? ... makes no use of inheritance. The function ?selectMethod? ... makes full use of the method dispatch mechanism; 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
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On Sun, May 23, 2010 at 5:25 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 05/22/2010 03:46 PM, Peng Yu wrote: >> On Sat, May 22, 2010 at 4:40 PM, Vincent Carey >> <stvjc at="" channing.harvard.edu=""> wrote: >>> 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") >> >> Why the following command doesn't work for 'quality'? >> >>> getMethod('quality', 'ShortReadQ') >> Error in getMethod("quality", "ShortReadQ") : No method found for >> function "quality" and signature ShortReadQ >>> showMethods('quality') >> Function: quality (package Biostrings) x="ANY" x="FastqQuality" >> (inherited from: x="ANY") x="ShortReadQ" (inherited from: x="ANY") > > see ?getMethod and the difference between selectMethod and getMethod, > conveniently documented on the same page. > > ? ? A call to ?getMethod? ... makes no use of inheritance. > > ? ? The function ?selectMethod? ... makes full use of the method > ? ? dispatch mechanism; Let me explain what I understand. Would you please let me know if my understanding is correct? quality is defined for signature 'ANY'. 'ShortReadQ' is inherited from 'ANY'. Since getMethod doesn't use inheritance, "getMethod('quality', 'ShortReadQ')" will not show retrieve the correct the function, right? I also see the class 'derivedDefaultMethod', where is it defined? > selectMethod(quality, 'ShortReadQ') Method Definition (Class "derivedDefaultMethod"): function (x) x at quality <environment: namespace:biostrings=""> Signatures: x target "ShortReadQ" defined "ANY" -- Regards, Peng
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