rTANDEM package -- An R encapsulation of the X!Tandem algorithm
1
1
Entering edit mode
@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
0
Entering edit mode
@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
0
Entering edit mode
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
1
Entering edit mode
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