From Cyrille.laurent.sage at gmail.com Wed Apr 1 16:28:28 2015 From: Cyrille.laurent.sage at gmail.com (Papysounours) Date: Wed, 1 Apr 2015 07:28:28 -0700 (PDT) Subject: [datatable-help] merging output to one data file Message-ID: <1427898508678-4705396.post@n4.nabble.com> Hi I wrote this small script in order to be able to analyze read from CHIP seq data. This script allow me to get from one read sequence all the possible combination by removing a base at each side of the read until no base are left. my issue is that I dont find the way to pull all the output into one csv or xls file with the name of the sample (read name) and the full list of combination.script#j=1#nr<-nrow(seq2)#n=1#while (n From joaomlanna at gmail.com Fri Apr 10 21:30:34 2015 From: joaomlanna at gmail.com (LANNA) Date: Fri, 10 Apr 2015 12:30:34 -0700 (PDT) Subject: [datatable-help] Fitting graphics to window Message-ID: <1428694234731-4705712.post@n4.nabble.com> Dear all, My Rstudio is creating graphics, which are not fitting with the window. Moreover, when I'm exporting it, it's looking like it was cut. I'm sending one example. How can I fit it and make it export the whole graphic? Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Fitting-graphics-to-window-tp4705712.html Sent from the datatable-help mailing list archive at Nabble.com. From rdpmachado at gmail.com Tue Apr 14 13:24:59 2015 From: rdpmachado at gmail.com (RMach) Date: Tue, 14 Apr 2015 04:24:59 -0700 (PDT) Subject: [datatable-help] jaccard index calculation Message-ID: <1429010699639-4705824.post@n4.nabble.com> Hi all, how should the input matrix structure be in order to use vegdist(vegan) to compute jaccard index. thanks in advance. RMach -- View this message in context: http://r.789695.n4.nabble.com/jaccard-index-calculation-tp4705824.html Sent from the datatable-help mailing list archive at Nabble.com. From benweinstein2010 at gmail.com Tue Apr 14 15:51:18 2015 From: benweinstein2010 at gmail.com (Ben Weinstein) Date: Tue, 14 Apr 2015 06:51:18 -0700 Subject: [datatable-help] jaccard index calculation In-Reply-To: <1429010699639-4705824.post@n4.nabble.com> References: <1429010699639-4705824.post@n4.nabble.com> Message-ID: Hi, Just following up on RMach's question with a bit on an example and further explanation since this is something i've always wondered about. I often find myself trying to compute pairwise distances on a series of rows. For each we have a keyed data.table that has 5000 columns and 10,000 row, which equates to (n*n-1)/2 comparisons ~ about 50 million in this case. The basic data structure and design looks like this: library(reshape2) a<-data.frame(ID=1:10,Site1=rbinom(1,1,.5),Site2=rbinom(10,1,.5),Site3=rbinom(10,1,0.5)) dista<-dist(a[,-1]) pairwise<-melt(as.matrix(dista)) colnames(pairwise)<-c("To","From","Dist") head(pairwise) We use a parallel computing strategy to chunk pieces, but its a real mess keeping track. The goal would be to find a data.table solution, especially one that does not repeat pairwise comparisons. For example, comparing row 4 to row 9 is the same as 9 to 4. The same could be done for any dist metric, including the vegdist vegan function. Thanks for your thoughts, Ben On Tue, Apr 14, 2015 at 4:24 AM, RMach wrote: > Hi all, > > how should the input matrix structure be in order to use vegdist(vegan) to > compute jaccard index. > > thanks in advance. > RMach > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/jaccard-index-calculation-tp4705824.html > Sent from the datatable-help mailing list archive at Nabble.com. > _______________________________________________ > datatable-help mailing list > datatable-help at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help > -- Ben Weinstein PhD Candidate Ecology and Evolution Stony Brook University http://benweinstein.weebly.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From statquant at outlook.com Fri Apr 17 12:59:39 2015 From: statquant at outlook.com (statquant3) Date: Fri, 17 Apr 2015 03:59:39 -0700 (PDT) Subject: [datatable-help] does fread read gz files yet ? Message-ID: <1429268379375-4705980.post@n4.nabble.com> Can't get this answer from google... -- View this message in context: http://r.789695.n4.nabble.com/does-fread-read-gz-files-yet-tp4705980.html Sent from the datatable-help mailing list archive at Nabble.com. From statquant at outlook.com Fri Apr 17 13:19:34 2015 From: statquant at outlook.com (statquant3) Date: Fri, 17 Apr 2015 04:19:34 -0700 (PDT) Subject: [datatable-help] using sep2 in fread Message-ID: <1429269574630-4705982.post@n4.nabble.com> I am trying to use sep2 in fread I have a file like a,b,c,d,e,f 12,12,12,a_21_r,12,12 12,12,12,a_21_r,12,13 12,12,12,a_21_r,12,14 12,12,12,a_21_r,12,15 I was hoping that fread could load me the file as a b c d e f 1: 12 12 12 (a,21,r) 12 12 2: 12 12 12 (a,21,r) 12 13 3: 12 12 12 (a,21,r) 12 14 4: 12 12 12 (a,21,r) 12 15 I can't have it working... -- View this message in context: http://r.789695.n4.nabble.com/using-sep2-in-fread-tp4705982.html Sent from the datatable-help mailing list archive at Nabble.com. From statquant at outlook.com Fri Apr 17 17:31:38 2015 From: statquant at outlook.com (statquant3) Date: Fri, 17 Apr 2015 08:31:38 -0700 (PDT) Subject: [datatable-help] does fread read gz files yet ? In-Reply-To: References: <1429268379375-4705980.post@n4.nabble.com> Message-ID: <1429284698837-4705992.post@n4.nabble.com> doing fread('zcat filePath.gz') still works loadTableFromCsvFile <- function(csvFileName, verbose=FALSE, ...){ #add zcat if the file extention is gz input <- paste0(ifelse(str_sub(csvFileName,-2)=='gz','zcat ',''),csvFileName) #read the file dt <- fread(input,...) if(verbose) cat('Loaded',csvFileName,'\n') return(dt) } -- View this message in context: http://r.789695.n4.nabble.com/does-fread-read-gz-files-yet-tp4705980p4705992.html Sent from the datatable-help mailing list archive at Nabble.com. From statquant at outlook.com Sat Apr 18 13:09:59 2015 From: statquant at outlook.com (statquant3) Date: Sat, 18 Apr 2015 04:09:59 -0700 (PDT) Subject: [datatable-help] How can I create a FR on github Message-ID: <1429355399154-4706036.post@n4.nabble.com> Hello, I am some very simple feature request, mostly sugar that I think would be usefull to data.table. How can I create a FR on the github repo ? Cheers -- View this message in context: http://r.789695.n4.nabble.com/How-can-I-create-a-FR-on-github-tp4706036.html Sent from the datatable-help mailing list archive at Nabble.com. From fperickson at wisc.edu Sat Apr 18 14:40:43 2015 From: fperickson at wisc.edu (Frank Erickson) Date: Sat, 18 Apr 2015 08:40:43 -0400 Subject: [datatable-help] How can I create a FR on github In-Reply-To: <1429355399154-4706036.post@n4.nabble.com> References: <1429355399154-4706036.post@n4.nabble.com> Message-ID: This looks like the FAQ for you: https://github.com/Rdatatable/data.table/blob/master/Contributing.md along with this page (which works if you're logged in): https://github.com/Rdatatable/data.table/issues/new On Sat, Apr 18, 2015 at 7:09 AM, statquant3 wrote: > Hello, I am some very simple feature request, mostly sugar that I think > would > be usefull to data.table. > How can I create a FR on the github repo ? > > Cheers > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/How-can-I-create-a-FR-on-github-tp4706036.html > Sent from the datatable-help mailing list archive at Nabble.com. > _______________________________________________ > datatable-help mailing list > datatable-help at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help > -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jonesd289 at gmail.com Sun Apr 19 09:47:44 2015 From: t.jonesd289 at gmail.com (tjonesd289) Date: Sun, 19 Apr 2015 00:47:44 -0700 (PDT) Subject: [datatable-help] fread on thorn delimitted file Message-ID: <1429429664109-4706068.post@n4.nabble.com> Hello, I have server logs with thorn ( ? , or '\xc3\xbe' ) delimited files. They are quite large and I would prefer to open them with fread (I would like to use data.table to look at the data). However, fread says it does not support 2 byte delimiters. I can delimit with just '\xc3' [ a = fread(MY_FILE, sep='\xc3') ] , but all values in every column at the first ends up with the '\xbe' attached (i.e. the second byte of the thorn character). Is there any work around to this? I have yet to find a way to open these files with R, though the is a stackoverflow answer saying it is possible. Thanks! -- View this message in context: http://r.789695.n4.nabble.com/fread-on-thorn-delimitted-file-tp4706068.html Sent from the datatable-help mailing list archive at Nabble.com. From statquant at outlook.com Mon Apr 20 09:45:40 2015 From: statquant at outlook.com (statquant3) Date: Mon, 20 Apr 2015 00:45:40 -0700 (PDT) Subject: [datatable-help] change from 1.9.3 --> 1.9.4 Message-ID: <1429515940732-4706076.post@n4.nabble.com> I realized today that I could not subset data.tables on integer64... library(data.table) library(bit64) data.table(x=as.integer64(c(1429251312176839931,1429251312176839932,1429251312176839933)))[x %in% as.integer64(c(1429251312176839931,1429251312176839932))] Error in UseMethod("as.data.table") : no applicable method for 'as.data.table' applied to an object of class "integer64" Is that new ? -- View this message in context: http://r.789695.n4.nabble.com/change-from-1-9-3-1-9-4-tp4706076.html Sent from the datatable-help mailing list archive at Nabble.com. From statquant at outlook.com Mon Apr 20 13:39:48 2015 From: statquant at outlook.com (statquant3) Date: Mon, 20 Apr 2015 04:39:48 -0700 (PDT) Subject: [datatable-help] change from 1.9.3 --> 1.9.4 Message-ID: <1429529988501-4706115.post@n4.nabble.com> Is this a know change of behaviour ? R) data.table(x=c(1,2,3,4,5,6)) x 1: 1 2: 2 3: 3 4: 4 5: 5 6: 6 R) dt = data.table(x=c(1,2,3,4,5,6)) #I think this used to work in 1.9.3 R) dt[x==min(x)] Error in eval(expr, envir, enclos) : object 'x' not found #This is equivalent (when there is a single minimum) to this R) dt[which.min(x)] x 1: 1 #This works for sure R) dt[x==min(dt$x)] x 1: 1 -- View this message in context: http://r.789695.n4.nabble.com/change-from-1-9-3-1-9-4-tp4706115.html Sent from the datatable-help mailing list archive at Nabble.com. From gerald.jean at dgag.ca Mon Apr 20 14:13:08 2015 From: gerald.jean at dgag.ca (Gerald Jean) Date: Mon, 20 Apr 2015 12:13:08 +0000 Subject: [datatable-help] does fread read gz files yet ? In-Reply-To: <1429268379375-4705980.post@n4.nabble.com> References: <1429268379375-4705980.post@n4.nabble.com> Message-ID: <7889EDA06EB6454D92349FFF17BF790F4B26265D@PWPRIMX72.mvt.desjardins.com> Here is what I use on a Linux server: fread(input = sprintf("zcat %s", x), header = TRUE, sep = ",", stringsAsFactors = FALSE, drop = drop) "x" is the file name, works great. G?rald Gerald Jean, M. Sc. en statistiques Conseiller senior en statistiques Actuariat corporatif, Mod?lisation et Recherche Assurance de dommages Mouvement Desjardins L?vis (si?ge social) 418 835-4900, poste 5527639 1 877 835-4900, poste 5527639 T?l?copieur : 418 835-6657 Faites bonne impression et imprimez seulement au besoin! Ce courriel est confidentiel, peut ?tre prot?g? par le secret professionnel et est adress? exclusivement au destinataire. Il est strictement interdit ? toute autre personne de diffuser, distribuer ou reproduire ce message. Si vous l'avez re?u par erreur, veuillez imm?diatement le d?truire et aviser l'exp?diteur. Merci. -----Message d'origine----- De?: datatable-help-bounces at lists.r-forge.r-project.org [mailto:datatable-help-bounces at lists.r-forge.r-project.org] De la part de statquant3 Envoy??: 17 avril 2015 07:00 ??: datatable-help at lists.r-forge.r-project.org Objet?: [datatable-help] does fread read gz files yet ? Can't get this answer from google... -- View this message in context: http://r.789695.n4.nabble.com/does-fread-read-gz-files-yet-tp4705980.html Sent from the datatable-help mailing list archive at Nabble.com. _______________________________________________ datatable-help mailing list datatable-help at lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help From statquant at outlook.com Mon Apr 20 15:21:40 2015 From: statquant at outlook.com (statquant3) Date: Mon, 20 Apr 2015 06:21:40 -0700 (PDT) Subject: [datatable-help] does fread read gz files yet ? In-Reply-To: <7889EDA06EB6454D92349FFF17BF790F4B26265D@PWPRIMX72.mvt.desjardins.com> References: <1429268379375-4705980.post@n4.nabble.com> <7889EDA06EB6454D92349FFF17BF790F4B26265D@PWPRIMX72.mvt.desjardins.com> Message-ID: <1429536100539-4706129.post@n4.nabble.com> This won't work if the input is not a *gz file -- View this message in context: http://r.789695.n4.nabble.com/does-fread-read-gz-files-yet-tp4705980p4706129.html Sent from the datatable-help mailing list archive at Nabble.com.