From lennart at karssen.org Sun Apr 12 21:14:33 2015 From: lennart at karssen.org (L.C. Karssen) Date: Sun, 12 Apr 2015 21:14:33 +0200 Subject: [GenABEL-dev] [Genabel-commits] r1943 - pkg/OmicABEL/src/reshuffle In-Reply-To: <20150412065433.699F51876B4@r-forge.r-project.org> References: <20150412065433.699F51876B4@r-forge.r-project.org> Message-ID: <552AC419.1090406@karssen.org> Hi Sodbo, Thanks for your bugfix! I've added some minor comments below. On 12-04-15 08:54, noreply at r-forge.r-project.org wrote: > Author: sharapovsodbo > Date: 2015-04-12 08:54:30 +0200 (Sun, 12 Apr 2015) > New Revision: 1943 > > Modified: > pkg/OmicABEL/src/reshuffle/Parameters.cpp > pkg/OmicABEL/src/reshuffle/main.cpp > pkg/OmicABEL/src/reshuffle/makefile > pkg/OmicABEL/src/reshuffle/reshuffle.cpp > Log: > Version 0.34 > fixed bug with "--chi" options fixed (before "--chi=0" or "--chi" extracted SNPs with chi>=1) > fixed same bug with "--chi" "--dataslim" options fixed > fixed bug with "--outfile" option (before "--outfile" didn't work if "--chi" was used) > fixed bug with trait names output format > minor changes > > > > Modified: pkg/OmicABEL/src/reshuffle/Parameters.cpp > =================================================================== > --- pkg/OmicABEL/src/reshuffle/Parameters.cpp 2015-03-31 13:05:51 UTC (rev 1942) > +++ pkg/OmicABEL/src/reshuffle/Parameters.cpp 2015-04-12 06:54:30 UTC (rev 1943) > @@ -136,7 +136,7 @@ > {"traits",optional_argument,NULL,'t'}, > {"snps",optional_argument,NULL,'s'}, > {"herit",optional_argument,NULL,'e'}, > - {"chi",required_argument,NULL,'c'}, > + {"chi",optional_argument,NULL,'c'}, > {"dataslim",no_argument,NULL,'l'}, > {"outfile",required_argument,NULL,'o'}, > {NULL,0,NULL,0} > @@ -179,10 +179,12 @@ > } > case 'c':{ > chi = Parameter(optarg,"chi"); > - if (chi.numbersset.size()==0){ > - cout<<"\nChi value is not a number. Please, set correct Chi value"; I would change "Chi" to "Chi^2" in the printed text (both here and further down) if I were you in order to avoid any confusion (I assume this is a Chi^2 cut-off value). You may want to consider changing the option name from --chi to --chi2, although I certainly understand it if you don't want to break existing scripts. Up to you. Thanks again for your contributions to the GenABEL project. Lennart. > + //cout << "\n\nchi.numbersset = " << chi<<"\n\n"; > + /*if (chi.numbersset.size()==0){ > + cout<<"\nChi value is not a number. Please, set correct Chi value\n"; > exit(1); > - } > + }*/ > + //cout <<"\nChi is yopta " << chi; > > break; > } > @@ -193,6 +195,7 @@ > case 'o':{ > default_outfile = false; > outfile=optarg; > + //cout << "\n\nOutfile name os yopta = " << outfile<<"\n\n"; > break; > } > } > > Modified: pkg/OmicABEL/src/reshuffle/main.cpp > =================================================================== > --- pkg/OmicABEL/src/reshuffle/main.cpp 2015-03-31 13:05:51 UTC (rev 1942) > +++ pkg/OmicABEL/src/reshuffle/main.cpp 2015-04-12 06:54:30 UTC (rev 1943) > @@ -49,7 +49,7 @@ > > cout<<"\nStart reshuffeling"; > iout_file iout_F(Params); > - cout << "\nFinish iout_file read\t" << double(clock()) / CLOCKS_PER_SEC <<" sec"; > + cout << "\nFinish iout_file read " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > > if(Params.traits.use) > Params.traits.setbynames(*(iout_F.labels.trait_names)); > @@ -59,7 +59,7 @@ > Params.herit.setbynames(*(iout_F.labels.trait_names)); > Reshuffle reshh(iout_F,Params); > reshh.run(); > - cout << "\nFinish reshuffling " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > - } > + cout << "\nFinish reshuffling " << double(clock()) / CLOCKS_PER_SEC <<" sec\n\n"; > + } > return (0); > } > > Modified: pkg/OmicABEL/src/reshuffle/makefile > =================================================================== > --- pkg/OmicABEL/src/reshuffle/makefile 2015-03-31 13:05:51 UTC (rev 1942) > +++ pkg/OmicABEL/src/reshuffle/makefile 2015-04-12 06:54:30 UTC (rev 1943) > @@ -3,12 +3,8 @@ > g++ -O3 -Wall -c -fmessage-length=0 -o reshuffle_obj.o reshuffle.cpp > g++ -O3 -Wall -c -fmessage-length=0 -o Parameters.o Parameters.cpp > g++ -O3 -Wall -c -fmessage-length=0 -o main.o main.cpp > - g++ -o reshuffle "reshuffle_obj.o" "main.o" "iout_file.o" "Parameters.o > + g++ -o reshuffle reshuffle_obj.o main.o iout_file.o Parameters.o > > clean: > > - del iout_file.o > - del reshuffle_obj.o > - del Parameters.o > - del main.o > - del reshuffle > \ No newline at end of file > + rm -rf *.o reshuffle > \ No newline at end of file > > Modified: pkg/OmicABEL/src/reshuffle/reshuffle.cpp > =================================================================== > --- pkg/OmicABEL/src/reshuffle/reshuffle.cpp 2015-03-31 13:05:51 UTC (rev 1942) > +++ pkg/OmicABEL/src/reshuffle/reshuffle.cpp 2015-04-12 06:54:30 UTC (rev 1943) > @@ -25,7 +25,7 @@ > txt_datadims << "Number of traits\t" << (*p_iout_file).header.t << endl; > txt_datadims << "Number of SNP\t" << (*p_iout_file).header.m << endl; > txt_datadims << "Number of covariates\t" << ((*p_iout_file).header.p - 2); > - cout<<"\nEnd write data dimension\t"<< double(clock()) / CLOCKS_PER_SEC <<" sec"; > + cout<<"\nEnd write data dimension "<< double(clock()) / CLOCKS_PER_SEC <<" sec"; > } > > void Reshuffle::write_snpnames(ofstream& txt_snpnames){ > @@ -36,8 +36,8 @@ > cout<<"\nWriting all SNP's names"; > } > for(set::iterator it= (*p_Parameters).snpnames.numbersset.begin();it!=(*p_Parameters).snpnames.numbersset.end();++it) > - txt_snpnames << "\nSNP #"<<(*it+1)<<"\t"<<(*(*p_iout_file).labels.snp_names)[*it]; > - cout<<"\nEnd write SNP's names\t" << double(clock()) / CLOCKS_PER_SEC <<" sec"; > + txt_snpnames << "\nSNP#"<<(*it+1)<<"\t"<<(*(*p_iout_file).labels.snp_names)[*it]; > + cout<<"\nEnd write SNP's names " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > } > > void Reshuffle::write_traitnames(ofstream& txt_traitnames){ > @@ -48,13 +48,13 @@ > cout<<"\nWriting all trait's names"; > } > for(std::set::iterator it= (*p_Parameters).traitnames.numbersset.begin();it!=p_Parameters->traitnames.numbersset.end();++it) > - txt_traitnames<<"TRAIT #"<<(*it+1)<<"\t"<<(*(*p_iout_file).labels.trait_names)[*it]; > - cout<<"\nEnd write trait's names\t" << double(clock()) / CLOCKS_PER_SEC <<" sec" << endl; > + txt_traitnames<<"\nTRAIT#"<<(*it+1)<<"\t"<<(*(*p_iout_file).labels.trait_names)[*it]; > + cout<<"\nEnd write trait's names " << double(clock()) / CLOCKS_PER_SEC <<" sec" << endl; > } > > void Reshuffle::write_data(ifstream& out_file,ofstream& data){ > out_file.seekg(0, ios_base::beg); > - cout << "\nStart write data\t" << double(clock()) / CLOCKS_PER_SEC <<" sec"; > + cout << "\nStart write data " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > data.precision(PRECISION_DOUBLE); > data<<"SNP\t"; > data<< "Trait\t"; > @@ -98,8 +98,13 @@ > out_file.seekg(0, ios_base::beg); > double chi = 0; > set::iterator chi_val = (*p_Parameters).chi.numbersset.begin(); > - double CheckChi = *chi_val+1; > - cout << "\nStart write chi data=" << double(clock()) / CLOCKS_PER_SEC <<" sec"; > + double CheckChi = 0; > + if((*p_Parameters).chi.numbersset.size()==0){ > + CheckChi = 0; > + }else{ > + CheckChi = *chi_val+1; > + } > + cout << "\nStart write chi data " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > txt_chi.precision(PRECISION_DOUBLE); > txt_chi << "SNP\t"; > txt_chi << "Trait\t"; > @@ -139,22 +144,27 @@ > ostr.clear(); > } > delete buf; > - cout << "\nFinish write chi data\t" << double(clock()) / CLOCKS_PER_SEC <<" sec"; > + cout << "\nFinish write chi data " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > } > > void Reshuffle::write_slim_data(ifstream& out_file, ofstream& txt_slim){ > - cout << "\nStart write slim data=" << double(clock()) / CLOCKS_PER_SEC <<" sec"; > + cout << "\nStart write slim data " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > out_file.seekg(0, ios_base::beg); > set goodtraits; > set goodsnps; > double chi = 0; > if((*p_Parameters).chi.def_value||(!(*p_Parameters).chi.use)){ > cout << "\nERROR: " << "Chi value doesn't exist"; > - cout << "\nPlease, set Chi value to get slim data"; > + cout << "\nPlease, set Chi value to get slim data\n"; > exit(1); > } > set::iterator chi_val = (*p_Parameters).chi.numbersset.begin(); > - double CheckChi = *chi_val+1; > + double CheckChi = 0; > + if((*p_Parameters).chi.numbersset.size()==0){ > + CheckChi = 0; > + }else{ > + CheckChi = *chi_val+1; > + } > double* buf = new double[per_trait_per_snp]; > for (set::iterator trait= (*p_Parameters).traits.numbersset.begin();trait!=(*p_Parameters).traits.numbersset.end();trait++) { > long long oldPos=0,pos = 0; > @@ -211,7 +221,7 @@ > ostr.clear(); > } > delete buf; > - cout <<"\nEnd write slim data\t" << double(clock()) / CLOCKS_PER_SEC <<" sec"; > + cout <<"\nEnd write slim data " << double(clock()) / CLOCKS_PER_SEC <<" sec"; > } > > int Reshuffle::est_shift(int counter){ > @@ -256,7 +266,7 @@ > out_file.seekg(est_shift(counter), ios_base::beg); > } > out_file.seekg(est_shift(3), ios_base::beg); > - for (unsigned int beta=0;beta<(*(p_iout_file->labels.beta)).size()-1;beta++) { > + for (unsigned int beta=0;beta<(*(p_iout_file->labels.beta)).size()-1;beta++) { > herest << (*(p_iout_file->labels).beta)[beta] << "\t"; > for (std::set::iterator trait= p_Parameters->herit.numbersset.begin();trait!=p_Parameters->herit.numbersset.end();trait++) { > out_file.read((char *) &tmp_number, sizeof(double)); > > _______________________________________________ > Genabel-commits mailing list > Genabel-commits at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From k.zhong at erasmusmc.nl Mon Apr 13 10:05:54 2015 From: k.zhong at erasmusmc.nl (K. Zhong) Date: Mon, 13 Apr 2015 08:05:54 +0000 Subject: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion In-Reply-To: References: <54EA473A.8040104@karssen.org> Message-ID: Dear all, I have read through the technical review guidelines and I think CollapsABEL satisfies all requirements except that `R CMD check` and `R CMD check -as-cran` both produces one warning and two notes. The warning is about my .git folder, which is for version control, and won?t be present once a binary package is built, so this is a non-issue. The notes are about some ?global variable? that are not global at all, and this is a known bug of `R CMD check` (see http://tinyurl.com/o9p6vxf for an example). So could anyone please review this package? The submission of our paper is waiting on this. Thanks! Best regards, Kaiyin ZHONG ------------------ FMB, Erasmus MC kaiyin.co.vu k.zhong at erasmusmc.nl kindlychung at gmail.com On 23/02/15 14:42, "K. Zhong" wrote: >Dear Lennart, > >At the moment I think it would be nice to keep the function as it is for >current users of it and show them a message about the new package. Thank >you for bringing this up. > >Best regards, >Kaiyin ZHONG >------------------ >FMB, Erasmus MC >kaiyin.co.vu >k.zhong at erasmusmc.nl >kindlychung at gmail.com > > > > > > > > >On 22/02/15 22:16, "L.C. Karssen" wrote: > >>Dear Kaiyin, >> >>Thank you for your willingness to contribute to the GenABEL project. >> >>On 19-02-15 14:27, K. Zhong wrote: >>> Dear all, >>> >>> I have recently finished an R package for compound heterozygosity >>> analysis for microarray/NGS data. This package (named CollapsABEL) >>> implements an extended version of the CDH test >>> >>>>>5 >>>> (see >>> DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user >>> friendly way and has already proved useful for our analysis with >>> certain dermatology traits. >> >>That sounds interesting indeed! To me it sounds like a useful addition >>to the GenABEL suite. >> >>> CDH test has been implemented before as a >>> function in the GenABEL package, but due to the simplicity of the >>>method >>> itself and restriction from the data format it uses, it is practically >>> not very useful. CollapsABEL overcomes these limitations and provides a >>> nice streamlined solution in your hands, for which reason I think it >>> would be a nice addition to the GenABEL family. >> >>Do you have a suggestion on what to do with the current CDH test in the >>GenABEL package? Is it worth to spend time maintaining it, or should we >>replace it with a message pointing people to CollapsABEL (of course >>assuming CollapsABEL gets accepted into the GenaBEL suite)? >> >>> >>> The project is hosted on >>> bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview >>> The R manual and an extensive tutorial can be found here: >>> https://bitbucket.org/kindlychung/collapsabel/downloads >> >>Thank you for providing these links. >> >>> >>> If you are willing to review this package, please let me know. >> >>I hope someone will step forward to do this. If you don't get a reaction >>in the coming few weeks, please feel free to send a reminder to the list. >> >> >>Best regards, >> >>Lennart Karssen. >> >>> >>> >>> Best regards, >>> >>> Kaiyin ZHONG >>> ------------------ >>> FMB, Erasmus MC >>> kaiyin.co.vu >>> k.zhong at erasmusmc.nl >>> kindlychung at gmail.com >>> >>> >>> >>> >>> >>> _______________________________________________ >>> genabel-devel mailing list >>> genabel-devel at lists.r-forge.r-project.org >>> >>>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-dev >>>e >>>l >>> >> >>-- >>*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>L.C. Karssen >>Utrecht >>The Netherlands >> >>lennart at karssen.org >>http://blog.karssen.org >>GPG key ID: A88F554A >>-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >> > From lennart at karssen.org Tue Apr 14 11:24:17 2015 From: lennart at karssen.org (L.C. Karssen) Date: Tue, 14 Apr 2015 11:24:17 +0200 Subject: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion In-Reply-To: References: <54EA473A.8040104@karssen.org> Message-ID: <552CDCC1.2020802@karssen.org> Dear Kaiyin, On 13-04-15 10:05, K. Zhong wrote: > Dear all, > > I have read through the technical review guidelines Thank you for that. Also thanks for bringing CollapsABEL back to our attention, unfortunately it fell of my radar. > and I think > CollapsABEL satisfies all requirements except that `R CMD check` and `R > CMD check -as-cran` both produces one warning and two notes. The warning > is about my .git folder, which is for version control, and won?t be > present once a binary package is built, so this is a non-issue. I agree. > The notes > are about some ?global variable? that are not global at all, and this is a > known bug of `R CMD check` (see http://tinyurl.com/o9p6vxf for an > example). Aha. This is more reason for concern. From my own experience the CRAN staff is quite strickt. Thanks for looking into "prior art". Since the SE post you refer to is three years old and the GranovaGG package it relates to is now in CRAN, I agree that we should see if it gets accepted. However, be prepared to act in case of comments from CRAN. > > So could anyone please review this package? The submission of our paper is > waiting on this. Thanks! I will review the package today. I will also try to contact other potential reviewers directly. Best regards, Lennart. > > > Best regards, > Kaiyin ZHONG > ------------------ > FMB, Erasmus MC > kaiyin.co.vu > k.zhong at erasmusmc.nl > kindlychung at gmail.com > > > > > > > > > On 23/02/15 14:42, "K. Zhong" wrote: > >> Dear Lennart, >> >> At the moment I think it would be nice to keep the function as it is for >> current users of it and show them a message about the new package. Thank >> you for bringing this up. >> >> Best regards, >> Kaiyin ZHONG >> ------------------ >> FMB, Erasmus MC >> kaiyin.co.vu >> k.zhong at erasmusmc.nl >> kindlychung at gmail.com >> >> >> >> >> >> >> >> >> On 22/02/15 22:16, "L.C. Karssen" wrote: >> >>> Dear Kaiyin, >>> >>> Thank you for your willingness to contribute to the GenABEL project. >>> >>> On 19-02-15 14:27, K. Zhong wrote: >>>> Dear all, >>>> >>>> I have recently finished an R package for compound heterozygosity >>>> analysis for microarray/NGS data. This package (named CollapsABEL) >>>> implements an extended version of the CDH test >>>> >>>> >>> 5 >>>>> (see >>>> DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user >>>> friendly way and has already proved useful for our analysis with >>>> certain dermatology traits. >>> >>> That sounds interesting indeed! To me it sounds like a useful addition >>> to the GenABEL suite. >>> >>>> CDH test has been implemented before as a >>>> function in the GenABEL package, but due to the simplicity of the >>>> method >>>> itself and restriction from the data format it uses, it is practically >>>> not very useful. CollapsABEL overcomes these limitations and provides a >>>> nice streamlined solution in your hands, for which reason I think it >>>> would be a nice addition to the GenABEL family. >>> >>> Do you have a suggestion on what to do with the current CDH test in the >>> GenABEL package? Is it worth to spend time maintaining it, or should we >>> replace it with a message pointing people to CollapsABEL (of course >>> assuming CollapsABEL gets accepted into the GenaBEL suite)? >>> >>>> >>>> The project is hosted on >>>> bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview >>>> The R manual and an extensive tutorial can be found here: >>>> https://bitbucket.org/kindlychung/collapsabel/downloads >>> >>> Thank you for providing these links. >>> >>>> >>>> If you are willing to review this package, please let me know. >>> >>> I hope someone will step forward to do this. If you don't get a reaction >>> in the coming few weeks, please feel free to send a reminder to the list. >>> >>> >>> Best regards, >>> >>> Lennart Karssen. >>> >>>> >>>> >>>> Best regards, >>>> >>>> Kaiyin ZHONG >>>> ------------------ >>>> FMB, Erasmus MC >>>> kaiyin.co.vu >>>> k.zhong at erasmusmc.nl >>>> kindlychung at gmail.com >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> genabel-devel mailing list >>>> genabel-devel at lists.r-forge.r-project.org >>>> >>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-dev >>>> e >>>> l >>>> >>> >>> -- >>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>> L.C. Karssen >>> Utrecht >>> The Netherlands >>> >>> lennart at karssen.org >>> http://blog.karssen.org >>> GPG key ID: A88F554A >>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>> >> > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From lennart at karssen.org Thu Apr 16 15:09:49 2015 From: lennart at karssen.org (L.C. Karssen) Date: Thu, 16 Apr 2015 15:09:49 +0200 Subject: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion In-Reply-To: <552CDCC1.2020802@karssen.org> References: <54EA473A.8040104@karssen.org> <552CDCC1.2020802@karssen.org> Message-ID: <552FB49D.2030400@karssen.org> Dear Kaiyin, A quick update on the package review: I'm having some troubles with my R development environment. I hope to resolve them today so that I can continue with my review of your package. Lennart. On 14-04-15 11:24, L.C. Karssen wrote: > Dear Kaiyin, > > > On 13-04-15 10:05, K. Zhong wrote: >> Dear all, >> >> I have read through the technical review guidelines > > Thank you for that. Also thanks for bringing CollapsABEL back to our > attention, unfortunately it fell of my radar. > >> and I think >> CollapsABEL satisfies all requirements except that `R CMD check` and `R >> CMD check -as-cran` both produces one warning and two notes. The warning >> is about my .git folder, which is for version control, and won?t be >> present once a binary package is built, so this is a non-issue. > > I agree. > >> The notes >> are about some ?global variable? that are not global at all, and this is a >> known bug of `R CMD check` (see http://tinyurl.com/o9p6vxf for an >> example). > > Aha. This is more reason for concern. From my own experience the CRAN > staff is quite strickt. Thanks for looking into "prior art". Since the > SE post you refer to is three years old and the GranovaGG package it > relates to is now in CRAN, I agree that we should see if it gets > accepted. However, be prepared to act in case of comments from CRAN. > >> >> So could anyone please review this package? The submission of our paper is >> waiting on this. Thanks! > > I will review the package today. I will also try to contact other > potential reviewers directly. > > > Best regards, > > Lennart. > >> >> >> Best regards, >> Kaiyin ZHONG >> ------------------ >> FMB, Erasmus MC >> kaiyin.co.vu >> k.zhong at erasmusmc.nl >> kindlychung at gmail.com >> >> >> >> >> >> >> >> >> On 23/02/15 14:42, "K. Zhong" wrote: >> >>> Dear Lennart, >>> >>> At the moment I think it would be nice to keep the function as it is for >>> current users of it and show them a message about the new package. Thank >>> you for bringing this up. >>> >>> Best regards, >>> Kaiyin ZHONG >>> ------------------ >>> FMB, Erasmus MC >>> kaiyin.co.vu >>> k.zhong at erasmusmc.nl >>> kindlychung at gmail.com >>> >>> >>> >>> >>> >>> >>> >>> >>> On 22/02/15 22:16, "L.C. Karssen" wrote: >>> >>>> Dear Kaiyin, >>>> >>>> Thank you for your willingness to contribute to the GenABEL project. >>>> >>>> On 19-02-15 14:27, K. Zhong wrote: >>>>> Dear all, >>>>> >>>>> I have recently finished an R package for compound heterozygosity >>>>> analysis for microarray/NGS data. This package (named CollapsABEL) >>>>> implements an extended version of the CDH test >>>>> >>>>> >>>> 5 >>>>>> (see >>>>> DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user >>>>> friendly way and has already proved useful for our analysis with >>>>> certain dermatology traits. >>>> >>>> That sounds interesting indeed! To me it sounds like a useful addition >>>> to the GenABEL suite. >>>> >>>>> CDH test has been implemented before as a >>>>> function in the GenABEL package, but due to the simplicity of the >>>>> method >>>>> itself and restriction from the data format it uses, it is practically >>>>> not very useful. CollapsABEL overcomes these limitations and provides a >>>>> nice streamlined solution in your hands, for which reason I think it >>>>> would be a nice addition to the GenABEL family. >>>> >>>> Do you have a suggestion on what to do with the current CDH test in the >>>> GenABEL package? Is it worth to spend time maintaining it, or should we >>>> replace it with a message pointing people to CollapsABEL (of course >>>> assuming CollapsABEL gets accepted into the GenaBEL suite)? >>>> >>>>> >>>>> The project is hosted on >>>>> bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview >>>>> The R manual and an extensive tutorial can be found here: >>>>> https://bitbucket.org/kindlychung/collapsabel/downloads >>>> >>>> Thank you for providing these links. >>>> >>>>> >>>>> If you are willing to review this package, please let me know. >>>> >>>> I hope someone will step forward to do this. If you don't get a reaction >>>> in the coming few weeks, please feel free to send a reminder to the list. >>>> >>>> >>>> Best regards, >>>> >>>> Lennart Karssen. >>>> >>>>> >>>>> >>>>> Best regards, >>>>> >>>>> Kaiyin ZHONG >>>>> ------------------ >>>>> FMB, Erasmus MC >>>>> kaiyin.co.vu >>>>> k.zhong at erasmusmc.nl >>>>> kindlychung at gmail.com >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> genabel-devel mailing list >>>>> genabel-devel at lists.r-forge.r-project.org >>>>> >>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-dev >>>>> e >>>>> l >>>>> >>>> >>>> -- >>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>> L.C. Karssen >>>> Utrecht >>>> The Netherlands >>>> >>>> lennart at karssen.org >>>> http://blog.karssen.org >>>> GPG key ID: A88F554A >>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>>> >>> >> > > > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From k.zhong at erasmusmc.nl Thu Apr 16 18:40:40 2015 From: k.zhong at erasmusmc.nl (K. Zhong) Date: Thu, 16 Apr 2015 16:40:40 +0000 Subject: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion In-Reply-To: <552FB49D.2030400@karssen.org> References: <54EA473A.8040104@karssen.org> <552CDCC1.2020802@karssen.org> <552FB49D.2030400@karssen.org> Message-ID: Dear Lennart, Concerning the R CMD check notes I reported last time, they are solved by some hack found on stack overflow. The latest package passes all checks: https://bitbucket.org/kindlychung/collapsabel/downloads/CollapsABEL_0.9.2.t ar.gz Best regards, Kaiyin ZHONG ------------------ FMB, Erasmus MC kaiyin.co.vu k.zhong at erasmusmc.nl kindlychung at gmail.com On 16/04/15 15:09, "L.C. Karssen" wrote: >Dear Kaiyin, > >A quick update on the package review: I'm having some troubles with my R >development environment. I hope to resolve them today so that I can >continue with my review of your package. > > >Lennart. > >On 14-04-15 11:24, L.C. Karssen wrote: >> Dear Kaiyin, >> >> >> On 13-04-15 10:05, K. Zhong wrote: >>> Dear all, >>> >>> I have read through the technical review guidelines >> >> Thank you for that. Also thanks for bringing CollapsABEL back to our >> attention, unfortunately it fell of my radar. >> >>> and I think >>> CollapsABEL satisfies all requirements except that `R CMD check` and `R >>> CMD check -as-cran` both produces one warning and two notes. The >>>warning >>> is about my .git folder, which is for version control, and won?t be >>> present once a binary package is built, so this is a non-issue. >> >> I agree. >> >>> The notes >>> are about some ?global variable? that are not global at all, and this >>>is a >>> known bug of `R CMD check` (see http://tinyurl.com/o9p6vxf for an >>> example). >> >> Aha. This is more reason for concern. From my own experience the CRAN >> staff is quite strickt. Thanks for looking into "prior art". Since the >> SE post you refer to is three years old and the GranovaGG package it >> relates to is now in CRAN, I agree that we should see if it gets >> accepted. However, be prepared to act in case of comments from CRAN. >> >>> >>> So could anyone please review this package? The submission of our >>>paper is >>> waiting on this. Thanks! >> >> I will review the package today. I will also try to contact other >> potential reviewers directly. >> >> >> Best regards, >> >> Lennart. >> >>> >>> >>> Best regards, >>> Kaiyin ZHONG >>> ------------------ >>> FMB, Erasmus MC >>> kaiyin.co.vu >>> k.zhong at erasmusmc.nl >>> kindlychung at gmail.com >>> >>> >>> >>> >>> >>> >>> >>> >>> On 23/02/15 14:42, "K. Zhong" wrote: >>> >>>> Dear Lennart, >>>> >>>> At the moment I think it would be nice to keep the function as it is >>>>for >>>> current users of it and show them a message about the new package. >>>>Thank >>>> you for bringing this up. >>>> >>>> Best regards, >>>> Kaiyin ZHONG >>>> ------------------ >>>> FMB, Erasmus MC >>>> kaiyin.co.vu >>>> k.zhong at erasmusmc.nl >>>> kindlychung at gmail.com >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 22/02/15 22:16, "L.C. Karssen" wrote: >>>> >>>>> Dear Kaiyin, >>>>> >>>>> Thank you for your willingness to contribute to the GenABEL project. >>>>> >>>>> On 19-02-15 14:27, K. Zhong wrote: >>>>>> Dear all, >>>>>> >>>>>> I have recently finished an R package for compound heterozygosity >>>>>> analysis for microarray/NGS data. This package (named CollapsABEL) >>>>>> implements an extended version of the CDH test >>>>>> >>>>>> >>>>>>>>>>>814 >>>>>> 5 >>>>>>> (see >>>>>> DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user >>>>>> friendly way and has already proved useful for our analysis with >>>>>> certain dermatology traits. >>>>> >>>>> That sounds interesting indeed! To me it sounds like a useful >>>>>addition >>>>> to the GenABEL suite. >>>>> >>>>>> CDH test has been implemented before as a >>>>>> function in the GenABEL package, but due to the simplicity of the >>>>>> method >>>>>> itself and restriction from the data format it uses, it is >>>>>>practically >>>>>> not very useful. CollapsABEL overcomes these limitations and >>>>>>provides a >>>>>> nice streamlined solution in your hands, for which reason I think it >>>>>> would be a nice addition to the GenABEL family. >>>>> >>>>> Do you have a suggestion on what to do with the current CDH test in >>>>>the >>>>> GenABEL package? Is it worth to spend time maintaining it, or should >>>>>we >>>>> replace it with a message pointing people to CollapsABEL (of course >>>>> assuming CollapsABEL gets accepted into the GenaBEL suite)? >>>>> >>>>>> >>>>>> The project is hosted on >>>>>> bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview >>>>>> The R manual and an extensive tutorial can be found here: >>>>>> https://bitbucket.org/kindlychung/collapsabel/downloads >>>>> >>>>> Thank you for providing these links. >>>>> >>>>>> >>>>>> If you are willing to review this package, please let me know. >>>>> >>>>> I hope someone will step forward to do this. If you don't get a >>>>>reaction >>>>> in the coming few weeks, please feel free to send a reminder to the >>>>>list. >>>>> >>>>> >>>>> Best regards, >>>>> >>>>> Lennart Karssen. >>>>> >>>>>> >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Kaiyin ZHONG >>>>>> ------------------ >>>>>> FMB, Erasmus MC >>>>>> kaiyin.co.vu >>>>>> k.zhong at erasmusmc.nl >>>>>> kindlychung at gmail.com >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> genabel-devel mailing list >>>>>> genabel-devel at lists.r-forge.r-project.org >>>>>> >>>>>> >>>>>>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel- >>>>>>dev >>>>>> e >>>>>> l >>>>>> >>>>> >>>>> -- >>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >>>>> L.C. Karssen >>>>> Utrecht >>>>> The Netherlands >>>>> >>>>> lennart at karssen.org >>>>> http://blog.karssen.org >>>>> GPG key ID: A88F554A >>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >>>>> >>>> >>> >> >> >> >> _______________________________________________ >> genabel-devel mailing list >> genabel-devel at lists.r-forge.r-project.org >> >>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-deve >>l >> > >-- >*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >L.C. Karssen >Utrecht >The Netherlands > >lennart at karssen.org >http://blog.karssen.org >GPG key ID: A88F554A >-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >