rTANDEM package -- An R encapsulation of the X!Tandem algorithm
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@frederic-fournier-5663
Last seen 8.1 years ago
Dear Bioconductor users, I would like to announce the release of the new package rTANDEM on bioconductor. This package encapsulates the mass spectrometry indentification algorithm X!Tandem in R, making it possible to conduct a full ms-ms analysis in R and to use R datamining capacities to search the results. We hope that rTANDEM can become the center of a viable pipeline for ms-ms proteomics in R. Questions, suggestions, bug-reports, and feedback of any kind is more than welcome. Sincerely, Frederic Fournier
Proteomics rTANDEM Proteomics rTANDEM • 898 views
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@steve-lianoglou-2771
Last seen 28 days ago
United States
Hi Frederic, On Wed, Dec 19, 2012 at 10:36 AM, Frederic Fournier <frederic.bioinfo at="" gmail.com=""> wrote: > Dear Bioconductor users, > > I would like to announce the release of the new package rTANDEM on > bioconductor. > This package encapsulates the mass spectrometry indentification algorithm > X!Tandem in R, making it possible to conduct a full ms-ms analysis in R and > to use R datamining capacities to search the results. We hope that rTANDEM > can become the center of a viable pipeline for ms-ms proteomics in R. > > Questions, suggestions, bug-reports, and feedback of any kind is more than > welcome. Really cool! Thanks for putting this together ... I checked out the source code to skim the package and notice that you use data.table (good choice :-) I see, however, that you felt that you needed to resort to some hacks to get it to work correctly, for instance in `GetPeptides`, you have: ## Dummy declaration to prevent "no visible binding" note when using data.table subset: pep.id=prot.uid=uid=NULL rmpep.id, prot.uid, uid) ... But this shouldn't be necessary, so if there's a problem in data.table I'd like to fix it. I'm curious if you list data.table in your "Imports" field in your DESCRIPTION file, then `import(data.table)` in your NAMESPACE, is this still necessary? I don't think I've run into this problem before, so I'm hoping these small changes should do the trick. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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On 12/19/2012 08:32 AM, Steve Lianoglou wrote: > Hi Frederic, > > On Wed, Dec 19, 2012 at 10:36 AM, Frederic Fournier > <frederic.bioinfo at="" gmail.com=""> wrote: >> Dear Bioconductor users, >> >> I would like to announce the release of the new package rTANDEM on >> bioconductor. >> This package encapsulates the mass spectrometry indentification algorithm >> X!Tandem in R, making it possible to conduct a full ms-ms analysis in R and >> to use R datamining capacities to search the results. We hope that rTANDEM >> can become the center of a viable pipeline for ms-ms proteomics in R. >> >> Questions, suggestions, bug-reports, and feedback of any kind is more than >> welcome. > > Really cool! > > Thanks for putting this together ... I checked out the source code to > skim the package and notice that you use data.table (good choice :-) I > see, however, that you felt that you needed to resort to some hacks to > get it to work correctly, for instance in `GetPeptides`, you have: > > ## Dummy declaration to prevent "no visible binding" note when using > data.table subset: > pep.id=prot.uid=uid=NULL > rmpep.id, prot.uid, uid) > ... > > But this shouldn't be necessary, so if there's a problem in data.table > I'd like to fix it. > > I'm curious if you list data.table in your "Imports" field in your > DESCRIPTION file, then `import(data.table)` in your NAMESPACE, is this > still necessary? > > I don't think I've run into this problem before, so I'm hoping these > small changes should do the trick. I'm not sure, but I think this cannot be solved by import'ing data.table. Here df <- data.frame(xx=1:5) subset(df, xx > 2) would trigger the same kind of warning about "no visible binding for global variable ?xx?" because codetools (used by R CMD check) doesn't know about the local environment in which subset is being evaluated and xx is to be found, as illustrated with > library(codetools) > f = function() { df = data.frame(xx=1:5); subset(df, xx > 2) } > f() xx 3 3 4 4 5 5 > findGlobals(f) [1] "=" ">" ":" "{" "data.frame" [6] "subset" "xx" utils::globalVariables is another solution to this problem, but in some ways not very satisfactory (it excludes named variables from the warning, but at package-level scope instead of the function in which the variable is being used). Martin > > HTH, > -steve > -- 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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Ahh, yes. Frederic also emailed me offlist indicating that it was used to get around some warning (notice(?)) in R CMD CHECK, which is why I've never seen it: I don't submit packages often, but when I do ... I don't test them. Sincerely, The most interesting programmer in the world. ;-) On Wed, Dec 19, 2012 at 7:37 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 12/19/2012 08:32 AM, Steve Lianoglou wrote: >> >> Hi Frederic, >> >> On Wed, Dec 19, 2012 at 10:36 AM, Frederic Fournier >> <frederic.bioinfo at="" gmail.com=""> wrote: >>> >>> Dear Bioconductor users, >>> >>> I would like to announce the release of the new package rTANDEM on >>> bioconductor. >>> This package encapsulates the mass spectrometry indentification algorithm >>> X!Tandem in R, making it possible to conduct a full ms-ms analysis in R >>> and >>> to use R datamining capacities to search the results. We hope that >>> rTANDEM >>> can become the center of a viable pipeline for ms-ms proteomics in R. >>> >>> Questions, suggestions, bug-reports, and feedback of any kind is more >>> than >>> welcome. >> >> >> Really cool! >> >> Thanks for putting this together ... I checked out the source code to >> skim the package and notice that you use data.table (good choice :-) I >> see, however, that you felt that you needed to resort to some hacks to >> get it to work correctly, for instance in `GetPeptides`, you have: >> >> ## Dummy declaration to prevent "no visible binding" note when using >> data.table subset: >> pep.id=prot.uid=uid=NULL >> rmpep.id, prot.uid, uid) >> ... >> >> But this shouldn't be necessary, so if there's a problem in data.table >> I'd like to fix it. >> >> I'm curious if you list data.table in your "Imports" field in your >> DESCRIPTION file, then `import(data.table)` in your NAMESPACE, is this >> still necessary? >> >> I don't think I've run into this problem before, so I'm hoping these >> small changes should do the trick. > > > I'm not sure, but I think this cannot be solved by import'ing data.table. > Here > > df <- data.frame(xx=1:5) > subset(df, xx > 2) > > would trigger the same kind of warning about "no visible binding for global > variable ?xx?" because codetools (used by R CMD check) doesn't know about > the local environment in which subset is being evaluated and xx is to be > found, as illustrated with > >> library(codetools) >> f = function() { df = data.frame(xx=1:5); subset(df, xx > 2) } >> f() > xx > 3 3 > 4 4 > 5 5 >> findGlobals(f) > [1] "=" ">" ":" "{" "data.frame" > [6] "subset" "xx" > > utils::globalVariables is another solution to this problem, but in some ways > not very satisfactory (it excludes named variables from the warning, but at > package-level scope instead of the function in which the variable is being > used). > > Martin > > >> >> HTH, >> -steve >> > > > -- > 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 -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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