From wentingwu.wwt at gmail.com Tue Mar 17 23:09:14 2015 From: wentingwu.wwt at gmail.com (wenting) Date: Tue, 17 Mar 2015 18:09:14 -0400 Subject: [GenABEL-dev] Question on ProbABEL output Message-ID: <5508A60A.7060307@gmail.com> Hi, Have one question about ProbABEL output. I browsed the manual and didn't find definition about the "beta_SNP_add" column. 1. What's the predicted Allele in this test, is it allele1? 2. How to define this beta value. Thanks! From lennart at karssen.org Wed Mar 18 09:42:52 2015 From: lennart at karssen.org (L.C. Karssen) Date: Wed, 18 Mar 2015 09:42:52 +0100 Subject: [GenABEL-dev] Question on ProbABEL output In-Reply-To: <5508A60A.7060307@gmail.com> References: <5508A60A.7060307@gmail.com> Message-ID: <55093A8C.7030400@karssen.org> Hi Wenting, Thank you for your interest in ProbABEL. This mailing list is used for development discussions. User support is normally done via our forum at http://forum.genabel.org, so please use that for any follow up questions you may have. Having said that, see below for an answer to your question. On 17-03-15 23:09, wenting wrote: > Hi, > > Have one question about ProbABEL output. > I browsed the manual and didn't find definition about the "beta_SNP_add" > column. > 1. What's the predicted Allele in this test, is it allele1? _add stands for additive. If you use probability files as input (with the --ngpreds=2 option), you'll get files for other genetic models as well (e.g. recessive and dominant), which have column names like beta_SNP_dom. The A1 allele is the predictor allele. > 2. How to define this beta value. I'm not sure what you mean with this question. In case of for example the phenotype height and the additive genetic model, a beta of 3 for a SNP with alleles A1=A and A2=T means that people with one copy of the T allele (AT) are on average 3 cm (assuming height was measured in cm) taller than people with the AA genotype. Similarly, people with TT are in general 2?3=6cm taller. Said differently: each copy of the T allele adds 3 cm to a person's height. Is this what you meant with your question? Best, Lennart. > > Thanks! > > _______________________________________________ > 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 yurii.aulchenko at gmail.com Mon Mar 30 19:35:52 2015 From: yurii.aulchenko at gmail.com (Yurii Aulchenko) Date: Mon, 30 Mar 2015 19:35:52 +0200 Subject: [GenABEL-dev] [Genabel-commits] r1938 - pkg/DatABEL/R In-Reply-To: <20150330154756.AA9921877FF@r-forge.r-project.org> References: <20150330154756.AA9921877FF@r-forge.r-project.org> Message-ID: <5D8933BA-583B-40A9-9610-92169A5832D7@gmail.com> Why not commenting this out (and keeping the commented code) - so we remember that in principle we want this functionality. Yurii > On 30 Mar 2015, at 17:47, noreply at r-forge.r-project.org wrote: > > Author: lckarssen > Date: 2015-03-30 17:47:56 +0200 (Mon, 30 Mar 2015) > New Revision: 1938 > > Modified: > pkg/DatABEL/R/zzz.R > Log: > DatABEL: Removed all internet accesses from the .onAttach() function as requested by Prof. Ripley. > > > Modified: pkg/DatABEL/R/zzz.R > =================================================================== > --- pkg/DatABEL/R/zzz.R 2015-03-30 15:37:47 UTC (rev 1937) > +++ pkg/DatABEL/R/zzz.R 2015-03-30 15:47:56 UTC (rev 1938) > @@ -2,51 +2,6 @@ > pkgVersion <- "0.9-6" > welcomeMessage <- paste0(pkg, " v.", pkgVersion," loaded\n") > > - ## check for news > - address <- c( > - "http://genabel.r-forge.r-project.org/version_and_news.html", > - "http://www.genabel.org/sites/default/files/version_and_news.html" > - ) > - svtmo <- options("timeout") > - options("timeout"=2) > - tryRes1 <- 0; class(tryRes1) <- "try-error" > - curaddr <- 1 > - while (class(tryRes1) == "try-error" && curaddr <= length(address) ) { > - suppressWarnings( > - tryRes0 <- try(conn <- url(address[curaddr]), silent=TRUE) > - ) > - suppressWarnings( > - tryRes1 <- try(fulltext <- readLines(conn), silent=TRUE) > - ) > - close(conn) > - curaddr <- curaddr + 1 > - } > - if (class(tryRes1) != "try-error") { > - if (length(fulltext)>0) > - { > - ## message to all users > - strnews <- grep("", tolower(fulltext)) > - endnews <- grep("", tolower(fulltext)) > - if (length(strnews) > 0 && length(endnews) > 0) > - if ((endnews-1) >= (strnews+1)) { > - welcomeMessage <- paste(welcomeMessage, > - fulltext[(strnews+1):(endnews-1)], > - sep="\n") > - } > - ## check for specific package news > - strnews <- grep(paste("<", pkg,"news>", sep=""), tolower(fulltext)) > - endnews <- grep(paste("", sep=""), tolower(fulltext)) > - if (length(strnews)>0 && length(endnews)>0) > - if ((endnews-1) >= (strnews+1)) { > - welcomeMessage <- paste(welcomeMessage, > - fulltext[(strnews+1):(endnews-1)], > - sep="\n") > - } > - } > - ##rm(a,fulltext,ver) > - } > - options("timeout"=svtmo) > - > .Call("checkNumBits"); > packageStartupMessage(welcomeMessage) > } > > _______________________________________________ > 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 From lennart at karssen.org Mon Mar 30 22:26:12 2015 From: lennart at karssen.org (L.C. Karssen) Date: Mon, 30 Mar 2015 22:26:12 +0200 Subject: [GenABEL-dev] [Genabel-commits] r1938 - pkg/DatABEL/R In-Reply-To: <5D8933BA-583B-40A9-9610-92169A5832D7@gmail.com> References: <20150330154756.AA9921877FF@r-forge.r-project.org> <5D8933BA-583B-40A9-9610-92169A5832D7@gmail.com> Message-ID: <5519B164.6010407@karssen.org> Hi Yurii, On 30-03-15 19:35, Yurii Aulchenko wrote: > Why not commenting this out (and keeping the commented code) - so we > remember that in principle we want this functionality. Then I'd rather insert a short comment pointing to this commit. That's why we have a version control system. Otherwise the source files get filled more and more with commented code that may be useful, once was useful, never worked but might be interesting, etc. Or I could add it as a Feature Request in the tracker. Lennart. > > Yurii > >> On 30 Mar 2015, at 17:47, noreply at r-forge.r-project.org wrote: >> >> Author: lckarssen Date: 2015-03-30 17:47:56 +0200 (Mon, 30 Mar >> 2015) New Revision: 1938 >> >> Modified: pkg/DatABEL/R/zzz.R Log: DatABEL: Removed all internet >> accesses from the .onAttach() function as requested by Prof. >> Ripley. >> >> >> Modified: pkg/DatABEL/R/zzz.R >> =================================================================== >> >> --- pkg/DatABEL/R/zzz.R 2015-03-30 15:37:47 UTC (rev 1937) >> +++ pkg/DatABEL/R/zzz.R 2015-03-30 15:47:56 UTC (rev 1938) @@ -2,51 >> +2,6 @@ pkgVersion <- "0.9-6" welcomeMessage <- paste0(pkg, " v.", >> pkgVersion," loaded\n") >> >> - ## check for news - address <- c( - >> "http://genabel.r-forge.r-project.org/version_and_news.html", - >> "http://www.genabel.org/sites/default/files/version_and_news.html" >> - ) - svtmo <- options("timeout") - options("timeout"=2) - >> tryRes1 <- 0; class(tryRes1) <- "try-error" - curaddr <- 1 - >> while (class(tryRes1) == "try-error" && curaddr <= length(address) >> ) { - suppressWarnings( - tryRes0 <- try(conn <- >> url(address[curaddr]), silent=TRUE) - ) - >> suppressWarnings( - tryRes1 <- try(fulltext <- >> readLines(conn), silent=TRUE) - ) - close(conn) - >> curaddr <- curaddr + 1 - } - if (class(tryRes1) != "try-error") >> { - if (length(fulltext)>0) - { - ## message to all >> users - strnews <- grep("", >> tolower(fulltext)) - endnews <- grep("", >> tolower(fulltext)) - if (length(strnews) > 0 && >> length(endnews) > 0) - if ((endnews-1) >= (strnews+1)) { - >> welcomeMessage <- paste(welcomeMessage, - >> fulltext[(strnews+1):(endnews-1)], - >> sep="\n") - } - ## check for specific package news >> - strnews <- grep(paste("<", pkg,"news>", sep=""), >> tolower(fulltext)) - endnews <- grep(paste("> pkg,"news>", sep=""), tolower(fulltext)) - if >> (length(strnews)>0 && length(endnews)>0) - if ((endnews-1) >> >= (strnews+1)) { - welcomeMessage <- >> paste(welcomeMessage, - >> fulltext[(strnews+1):(endnews-1)], - >> sep="\n") - } - } - ##rm(a,fulltext,ver) - } - >> options("timeout"=svtmo) - .Call("checkNumBits"); >> packageStartupMessage(welcomeMessage) } >> >> _______________________________________________ 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 > >> > _______________________________________________ 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 yurii.aulchenko at gmail.com Tue Mar 31 13:12:07 2015 From: yurii.aulchenko at gmail.com (Yury Aulchenko) Date: Tue, 31 Mar 2015 13:12:07 +0200 Subject: [GenABEL-dev] [Genabel-commits] r1938 - pkg/DatABEL/R In-Reply-To: <5519B164.6010407@karssen.org> References: <20150330154756.AA9921877FF@r-forge.r-project.org> <5D8933BA-583B-40A9-9610-92169A5832D7@gmail.com> <5519B164.6010407@karssen.org> Message-ID: Ok, I am convinced :) ---------------- Sent from mobile device, please excuse possible typos > On 30 Mar 2015, at 22:26, L.C. Karssen wrote: > > Hi Yurii, > >> On 30-03-15 19:35, Yurii Aulchenko wrote: >> Why not commenting this out (and keeping the commented code) - so we >> remember that in principle we want this functionality. > > Then I'd rather insert a short comment pointing to this commit. That's > why we have a version control system. > Otherwise the source files get filled more and more with commented code > that may be useful, once was useful, never worked but might be > interesting, etc. > > Or I could add it as a Feature Request in the tracker. > > > Lennart. > >> >> Yurii >> >>> On 30 Mar 2015, at 17:47, noreply at r-forge.r-project.org wrote: >>> >>> Author: lckarssen Date: 2015-03-30 17:47:56 +0200 (Mon, 30 Mar >>> 2015) New Revision: 1938 >>> >>> Modified: pkg/DatABEL/R/zzz.R Log: DatABEL: Removed all internet >>> accesses from the .onAttach() function as requested by Prof. >>> Ripley. >>> >>> >>> Modified: pkg/DatABEL/R/zzz.R >>> =================================================================== > --- pkg/DatABEL/R/zzz.R 2015-03-30 15:37:47 UTC (rev 1937) >>> +++ pkg/DatABEL/R/zzz.R 2015-03-30 15:47:56 UTC (rev 1938) @@ -2,51 >>> +2,6 @@ pkgVersion <- "0.9-6" welcomeMessage <- paste0(pkg, " v.", >>> pkgVersion," loaded\n") >>> >>> - ## check for news - address <- c( - >>> "http://genabel.r-forge.r-project.org/version_and_news.html", - >>> "http://www.genabel.org/sites/default/files/version_and_news.html" >>> - ) - svtmo <- options("timeout") - options("timeout"=2) - >>> tryRes1 <- 0; class(tryRes1) <- "try-error" - curaddr <- 1 - >>> while (class(tryRes1) == "try-error" && curaddr <= length(address) >>> ) { - suppressWarnings( - tryRes0 <- try(conn <- >>> url(address[curaddr]), silent=TRUE) - ) - >>> suppressWarnings( - tryRes1 <- try(fulltext <- >>> readLines(conn), silent=TRUE) - ) - close(conn) - >>> curaddr <- curaddr + 1 - } - if (class(tryRes1) != "try-error") >>> { - if (length(fulltext)>0) - { - ## message to all >>> users - strnews <- grep("", >>> tolower(fulltext)) - endnews <- grep("", >>> tolower(fulltext)) - if (length(strnews) > 0 && >>> length(endnews) > 0) - if ((endnews-1) >= (strnews+1)) { - >>> welcomeMessage <- paste(welcomeMessage, - >>> fulltext[(strnews+1):(endnews-1)], - >>> sep="\n") - } - ## check for specific package news >>> - strnews <- grep(paste("<", pkg,"news>", sep=""), >>> tolower(fulltext)) - endnews <- grep(paste(">> pkg,"news>", sep=""), tolower(fulltext)) - if >>> (length(strnews)>0 && length(endnews)>0) - if ((endnews-1) >>>> = (strnews+1)) { - welcomeMessage <- >>> paste(welcomeMessage, - >>> fulltext[(strnews+1):(endnews-1)], - >>> sep="\n") - } - } - ##rm(a,fulltext,ver) - } - >>> options("timeout"=svtmo) - .Call("checkNumBits"); >>> packageStartupMessage(welcomeMessage) } >>> >>> _______________________________________________ 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 >> >> _______________________________________________ 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 > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > _______________________________________________ > 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