From noreply at r-forge.r-project.org Tue May 13 11:19:44 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 13 May 2014 11:19:44 +0200 (CEST) Subject: [Patchwork-commits] r207 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/TAPS/R Message-ID: <20140513091944.E5389186CEB@r-forge.r-project.org> Author: sebastian_d Date: 2014-05-13 11:19:44 +0200 (Tue, 13 May 2014) New Revision: 207 Modified: .git/COMMIT_EDITMSG .git/index .git/logs/HEAD .git/logs/refs/heads/master .git/logs/refs/remotes/origin/master .git/refs/heads/master .git/refs/remotes/origin/master pkg/TAPS/R/TAPS.r Log: Bjorn update Modified: .git/COMMIT_EDITMSG =================================================================== --- .git/COMMIT_EDITMSG 2014-04-28 13:41:46 UTC (rev 206) +++ .git/COMMIT_EDITMSG 2014-05-13 09:19:44 UTC (rev 207) @@ -1 +1 @@ -Big upgrades to homepage and genelist +hotfix cy750K Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2014-04-28 13:41:46 UTC (rev 206) +++ .git/logs/HEAD 2014-05-13 09:19:44 UTC (rev 207) @@ -88,3 +88,5 @@ 53a860b490c7ac5501d8bb4f6b95e700491e12d4 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 Sebastian DiLorenzo 1395307764 +0100 pull: Merge made by the 'recursive' strategy. 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo 1395830196 +0100 pull: Fast-forward 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo 1398692432 +0200 pull: Fast-forward +cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399362996 +0200 commit: hotfix cy750K +3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: Fast-forward Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2014-04-28 13:41:46 UTC (rev 206) +++ .git/logs/refs/heads/master 2014-05-13 09:19:44 UTC (rev 207) @@ -88,3 +88,5 @@ 53a860b490c7ac5501d8bb4f6b95e700491e12d4 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 Sebastian DiLorenzo 1395307764 +0100 pull: Merge made by the 'recursive' strategy. 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo 1395830196 +0100 pull: Fast-forward 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo 1398692432 +0200 pull: Fast-forward +cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399362996 +0200 commit: hotfix cy750K +3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: Fast-forward Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2014-04-28 13:41:46 UTC (rev 206) +++ .git/logs/refs/remotes/origin/master 2014-05-13 09:19:44 UTC (rev 207) @@ -85,3 +85,5 @@ bf30fc707ee93417a8fad1f8ab1d8dc7426e128a 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 Sebastian DiLorenzo 1395307814 +0100 update by push 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo 1395830195 +0100 pull: fast-forward 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo 1398692432 +0200 pull: fast-forward +cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399363003 +0200 update by push +3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: fast-forward Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2014-04-28 13:41:46 UTC (rev 206) +++ .git/refs/heads/master 2014-05-13 09:19:44 UTC (rev 207) @@ -1 +1 @@ -cb2b4bc53aac68ec1b56532dbbded71b4eca7582 +18800d736527a84881558f1f00ba4af0f62807fe Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2014-04-28 13:41:46 UTC (rev 206) +++ .git/refs/remotes/origin/master 2014-05-13 09:19:44 UTC (rev 207) @@ -1 +1 @@ -cb2b4bc53aac68ec1b56532dbbded71b4eca7582 +18800d736527a84881558f1f00ba4af0f62807fe Modified: pkg/TAPS/R/TAPS.r =================================================================== --- pkg/TAPS/R/TAPS.r 2014-04-28 13:41:46 UTC (rev 206) +++ pkg/TAPS/R/TAPS.r 2014-05-13 09:19:44 UTC (rev 207) @@ -84,7 +84,7 @@ # print(paste(i,': ',subs[i],': Opening',sep='')) print(paste(i,'/',length(subs),': ',subs[i],' Loading',sep='')) - if(length(grep("*.cyhd.cychp",dir()))==1) ##cyhd sample + if(length(grep("*.cychp",dir()))==1) ##cychp sample { ##read CYCHP file from ChAS with log-ratio info## ################################################ @@ -120,7 +120,7 @@ ##read txt file from ChAS with snp info## ######################################### - name=list.files(".",pattern="*.cyhd.txt") + name=c(list.files(".",pattern="*.cy750K.txt"),list.files(".",pattern="*.cyhd.txt")) tempalf=read.table(file=name, header=FALSE, sep="\t", skip=12) SignalA=tempalf$V4 SignalB=tempalf$V5 @@ -388,7 +388,7 @@ setwd('..') } #save.txt(sampleData,file='sampleData.csv') - 1 + } ### regsFromSegs <- function (Log2,alf, segments, bin=200,min=1,matched=F,allelePeaks=FALSE) { @@ -455,7 +455,7 @@ } allelicImbalance <- function (data,min=30,matched=F,allelePeaks=F) { if(matched == T ) { - return(2*median(abs(data$Value-.5),na.rm=T)) + return(2*median(abs(data-.5),na.rm=T)) } if(allelePeaks == F) { if (length(data)>min) { ## Time to calculate Allelic Imbalance Ratio (if enough SNPs) @@ -3565,11 +3565,12 @@ #Wrapper for getEstimates(). It will execute getEstimates in every sample folder. #If SampleData.csv already exists it will create the file SampleData_YYYY-MM-DD_HH-MM-SS.csv instead. TAPS_estimates <- function(path=getwd()) { - library(foreach) - library(TAPS) + suppressPackageStartupMessages(library(foreach)) + suppressPackageStartupMessages(library(TAPS)) # setwd("/media/safe/COAD_TCGA/NexusTxtFiles/tumorCELFiles") root <- path - samples <- dir()[file.info(dir())$isdir] + samples <- dir(path)[file.info(cbind(paste(path,cbind(dir(path)),sep='/')))$isdir] + # samples <- dir(path)[file.info(path)$isdir] # samples <- samples[grep('^[A-Z]',samples)] datat <- foreach(sample=samples) %do% { setwd(paste(root,'/',sample,sep='')) @@ -3593,6 +3594,7 @@ file.rename('SampleData.csv',paste('SampleData',format(Sys.time(), "_old_TAPS_estimates_%F_%T.csv"),sep='')) } write.table(sampledata,'SampleData.csv',sep='\t',row.names=F) + print('OK') } @@ -3769,7 +3771,7 @@ miny <- 0.5170546 # sampleData <- read.csv('SampleData.csv',sep='\t',header=T,colClasses=c('character',rep('numeric',4)),stringsAsFactors=F) - sampleData <- read.csv('SampleData.csv',sep='\t',header=T,stringsAsFactors=F) + sampleData <- read.csv(paste(path,'SampleData.csv',sep='/'),sep='\t',header=T,stringsAsFactors=F) if(any(colnames(sampleData) %in% c('MAPD','MHOF'))) sampleData <- sampleData[,1:5] sampleDataOri <- sampleData From noreply at r-forge.r-project.org Tue May 13 15:11:37 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 13 May 2014 15:11:37 +0200 (CEST) Subject: [Patchwork-commits] r208 - pkg/TAPS/man www Message-ID: <20140513131137.DE671180524@r-forge.r-project.org> Author: sebastian_d Date: 2014-05-13 15:11:37 +0200 (Tue, 13 May 2014) New Revision: 208 Modified: pkg/TAPS/man/TAPS_call.Rd pkg/TAPS/man/TAPS_plot.Rd www/TAPS_inst.php Log: update regarding taps install and doMC2 Modified: pkg/TAPS/man/TAPS_call.Rd =================================================================== --- pkg/TAPS/man/TAPS_call.Rd 2014-05-13 09:19:44 UTC (rev 207) +++ pkg/TAPS/man/TAPS_call.Rd 2014-05-13 13:11:37 UTC (rev 208) @@ -25,7 +25,7 @@ Directory where the sample folders reside. Default is current directory. } \item{cores}{ - Default is 1. Set amount of threads/cores to be used. + Default is 1. Only supported on unix based systems. Set amount of threads/cores to be used. } } Modified: pkg/TAPS/man/TAPS_plot.Rd =================================================================== --- pkg/TAPS/man/TAPS_plot.Rd 2014-05-13 09:19:44 UTC (rev 207) +++ pkg/TAPS/man/TAPS_plot.Rd 2014-05-13 13:11:37 UTC (rev 208) @@ -42,7 +42,7 @@ Default is 400. } \item{cores}{ - Default is 1. Set amount of threads/cores to be used. + Default is 1. Only supported on unix based systems. Set amount of threads/cores to be used. } \item{matched}{ Default is FALSE. Set to TRUE if a matched normal has been used to remove homozygous snp allele frequencies. Modified: www/TAPS_inst.php =================================================================== --- www/TAPS_inst.php 2014-05-13 09:19:44 UTC (rev 207) +++ www/TAPS_inst.php 2014-05-13 13:11:37 UTC (rev 208) @@ -15,8 +15,10 @@ install.packages("affxparser") install.packages("fields") install.packages("foreach") + install.packages("jpeg") + + #Only on unix-based systems install.packages("doMC") - install.packages("jpeg") Install TAPS. From noreply at r-forge.r-project.org Tue May 13 15:13:38 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 13 May 2014 15:13:38 +0200 (CEST) Subject: [Patchwork-commits] r209 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/TAPS/R Message-ID: <20140513131338.6DB1F183FDA@r-forge.r-project.org> Author: sebastian_d Date: 2014-05-13 15:13:38 +0200 (Tue, 13 May 2014) New Revision: 209 Modified: .git/index .git/logs/HEAD .git/logs/refs/heads/master .git/logs/refs/remotes/origin/master .git/refs/heads/master .git/refs/remotes/origin/master pkg/TAPS/R/TAPS.r Log: bjorn update doMC Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2014-05-13 13:11:37 UTC (rev 208) +++ .git/logs/HEAD 2014-05-13 13:13:38 UTC (rev 209) @@ -90,3 +90,4 @@ 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo 1398692432 +0200 pull: Fast-forward cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399362996 +0200 commit: hotfix cy750K 3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: Fast-forward +18800d736527a84881558f1f00ba4af0f62807fe 933655cc7d8def1beddb1f60ed576d1653ef8504 Sebastian DiLorenzo 1399986792 +0200 pull: Fast-forward Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2014-05-13 13:11:37 UTC (rev 208) +++ .git/logs/refs/heads/master 2014-05-13 13:13:38 UTC (rev 209) @@ -90,3 +90,4 @@ 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo 1398692432 +0200 pull: Fast-forward cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399362996 +0200 commit: hotfix cy750K 3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: Fast-forward +18800d736527a84881558f1f00ba4af0f62807fe 933655cc7d8def1beddb1f60ed576d1653ef8504 Sebastian DiLorenzo 1399986792 +0200 pull: Fast-forward Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2014-05-13 13:11:37 UTC (rev 208) +++ .git/logs/refs/remotes/origin/master 2014-05-13 13:13:38 UTC (rev 209) @@ -87,3 +87,4 @@ 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo 1398692432 +0200 pull: fast-forward cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399363003 +0200 update by push 3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: fast-forward +18800d736527a84881558f1f00ba4af0f62807fe 933655cc7d8def1beddb1f60ed576d1653ef8504 Sebastian DiLorenzo 1399986792 +0200 pull: fast-forward Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2014-05-13 13:11:37 UTC (rev 208) +++ .git/refs/heads/master 2014-05-13 13:13:38 UTC (rev 209) @@ -1 +1 @@ -18800d736527a84881558f1f00ba4af0f62807fe +933655cc7d8def1beddb1f60ed576d1653ef8504 Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2014-05-13 13:11:37 UTC (rev 208) +++ .git/refs/remotes/origin/master 2014-05-13 13:13:38 UTC (rev 209) @@ -1 +1 @@ -18800d736527a84881558f1f00ba4af0f62807fe +933655cc7d8def1beddb1f60ed576d1653ef8504 Modified: pkg/TAPS/R/TAPS.r =================================================================== --- pkg/TAPS/R/TAPS.r 2014-05-13 13:11:37 UTC (rev 208) +++ pkg/TAPS/R/TAPS.r 2014-05-13 13:13:38 UTC (rev 209) @@ -25,8 +25,8 @@ suppressPackageStartupMessages(library(fields)) suppressPackageStartupMessages(library(xlsx)) suppressPackageStartupMessages(library(foreach)) - suppressPackageStartupMessages(library(doMC)) - suppressPackageStartupMessages(registerDoMC(cores=cores)) + try(suppressPackageStartupMessages(library(doMC)),silent=T) + try(suppressPackageStartupMessages(registerDoMC(cores=cores),silent=T) #list.of.packages <- c("stats", "fields") @@ -263,8 +263,8 @@ maxCn=12 #suppressPackageStartupMessages(library(xlsx)) suppressPackageStartupMessages(library(foreach)) - suppressPackageStartupMessages(library(doMC)) - suppressPackageStartupMessages(registerDoMC(cores=cores)) + try(suppressPackageStartupMessages(library(doMC)),silent=T) + try(suppressPackageStartupMessages(registerDoMC(cores=cores),silent=T) ## TAPS_call outputs the total and minor allele copy numbers of all segments as a text file, and as images for visual confirmation. From noreply at r-forge.r-project.org Wed May 14 11:00:32 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 14 May 2014 11:00:32 +0200 (CEST) Subject: [Patchwork-commits] r210 - pkg/TAPS/R Message-ID: <20140514090032.E5C1A187429@r-forge.r-project.org> Author: sebastian_d Date: 2014-05-14 11:00:31 +0200 (Wed, 14 May 2014) New Revision: 210 Modified: pkg/TAPS/R/TAPS.r Log: buggfix nr2 Modified: pkg/TAPS/R/TAPS.r =================================================================== --- pkg/TAPS/R/TAPS.r 2014-05-13 13:13:38 UTC (rev 209) +++ pkg/TAPS/R/TAPS.r 2014-05-14 09:00:31 UTC (rev 210) @@ -26,7 +26,7 @@ suppressPackageStartupMessages(library(xlsx)) suppressPackageStartupMessages(library(foreach)) try(suppressPackageStartupMessages(library(doMC)),silent=T) - try(suppressPackageStartupMessages(registerDoMC(cores=cores),silent=T) + try(suppressPackageStartupMessages(registerDoMC(cores=cores)),silent=T) #list.of.packages <- c("stats", "fields") @@ -264,7 +264,7 @@ #suppressPackageStartupMessages(library(xlsx)) suppressPackageStartupMessages(library(foreach)) try(suppressPackageStartupMessages(library(doMC)),silent=T) - try(suppressPackageStartupMessages(registerDoMC(cores=cores),silent=T) + try(suppressPackageStartupMessages(registerDoMC(cores=cores)),silent=T) ## TAPS_call outputs the total and minor allele copy numbers of all segments as a text file, and as images for visual confirmation. From noreply at r-forge.r-project.org Wed May 14 11:23:07 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 14 May 2014 11:23:07 +0200 (CEST) Subject: [Patchwork-commits] r211 - pkg/TAPS/man Message-ID: <20140514092307.4E9E3186A63@r-forge.r-project.org> Author: sebastian_d Date: 2014-05-14 11:23:07 +0200 (Wed, 14 May 2014) New Revision: 211 Modified: pkg/TAPS/man/TAPS_plot.Rd Log: documentation update taps Modified: pkg/TAPS/man/TAPS_plot.Rd =================================================================== --- pkg/TAPS/man/TAPS_plot.Rd 2014-05-14 09:00:31 UTC (rev 210) +++ pkg/TAPS/man/TAPS_plot.Rd 2014-05-14 09:23:07 UTC (rev 211) @@ -20,7 +20,7 @@ \usage{ -TAPS_plot(directory=NULL,autoEstimate=FALSE,bin=400,cores=1,matched=FALSE) +TAPS_plot(directory=NULL,autoEstimate=FALSE,bin=400,cores=1,matched=FALSE,allelePeaks=FALSE) } \arguments{ @@ -47,6 +47,9 @@ \item{matched}{ Default is FALSE. Set to TRUE if a matched normal has been used to remove homozygous snp allele frequencies. } + \item{allelePeaks}{ + Default is FALSE. Set to TRUE if SNP values are allele peaks, not B-allele frequency. + } } \details{ From noreply at r-forge.r-project.org Wed May 28 11:42:39 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 28 May 2014 11:42:39 +0200 (CEST) Subject: [Patchwork-commits] r212 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/TAPS/R Message-ID: <20140528094239.569A61812A9@r-forge.r-project.org> Author: sebastian_d Date: 2014-05-28 11:42:38 +0200 (Wed, 28 May 2014) New Revision: 212 Modified: .git/COMMIT_EDITMSG .git/index .git/logs/HEAD .git/logs/refs/heads/master .git/logs/refs/remotes/origin/master .git/refs/heads/master .git/refs/remotes/origin/master pkg/TAPS/R/TAPS.r Log: bjorn short fix Modified: .git/COMMIT_EDITMSG =================================================================== --- .git/COMMIT_EDITMSG 2014-05-14 09:23:07 UTC (rev 211) +++ .git/COMMIT_EDITMSG 2014-05-28 09:42:38 UTC (rev 212) @@ -1 +1 @@ -hotfix cy750K +update to TAPS installation information doMC windows Modified: .git/index =================================================================== (Binary files differ) Modified: .git/logs/HEAD =================================================================== --- .git/logs/HEAD 2014-05-14 09:23:07 UTC (rev 211) +++ .git/logs/HEAD 2014-05-28 09:42:38 UTC (rev 212) @@ -91,3 +91,7 @@ cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399362996 +0200 commit: hotfix cy750K 3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: Fast-forward 18800d736527a84881558f1f00ba4af0f62807fe 933655cc7d8def1beddb1f60ed576d1653ef8504 Sebastian DiLorenzo 1399986792 +0200 pull: Fast-forward +933655cc7d8def1beddb1f60ed576d1653ef8504 9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 Sebastian DiLorenzo 1399986838 +0200 commit: update to TAPS installation information doMC windows +9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 e244c2ac30341cbf8f109cc96f7661258e9baa93 Sebastian DiLorenzo 1400058009 +0200 pull: Fast-forward +e244c2ac30341cbf8f109cc96f7661258e9baa93 90e8ee38aac7ead43935bd7034bd4f11f91d19c4 Sebastian DiLorenzo 1400059317 +0200 pull: Fast-forward +90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo 1401270131 +0200 pull: Fast-forward Modified: .git/logs/refs/heads/master =================================================================== --- .git/logs/refs/heads/master 2014-05-14 09:23:07 UTC (rev 211) +++ .git/logs/refs/heads/master 2014-05-28 09:42:38 UTC (rev 212) @@ -91,3 +91,7 @@ cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399362996 +0200 commit: hotfix cy750K 3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: Fast-forward 18800d736527a84881558f1f00ba4af0f62807fe 933655cc7d8def1beddb1f60ed576d1653ef8504 Sebastian DiLorenzo 1399986792 +0200 pull: Fast-forward +933655cc7d8def1beddb1f60ed576d1653ef8504 9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 Sebastian DiLorenzo 1399986838 +0200 commit: update to TAPS installation information doMC windows +9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 e244c2ac30341cbf8f109cc96f7661258e9baa93 Sebastian DiLorenzo 1400058009 +0200 pull: Fast-forward +e244c2ac30341cbf8f109cc96f7661258e9baa93 90e8ee38aac7ead43935bd7034bd4f11f91d19c4 Sebastian DiLorenzo 1400059317 +0200 pull: Fast-forward +90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo 1401270131 +0200 pull: Fast-forward Modified: .git/logs/refs/remotes/origin/master =================================================================== --- .git/logs/refs/remotes/origin/master 2014-05-14 09:23:07 UTC (rev 211) +++ .git/logs/refs/remotes/origin/master 2014-05-28 09:42:38 UTC (rev 212) @@ -88,3 +88,7 @@ cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo 1399363003 +0200 update by push 3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo 1399972601 +0200 pull: fast-forward 18800d736527a84881558f1f00ba4af0f62807fe 933655cc7d8def1beddb1f60ed576d1653ef8504 Sebastian DiLorenzo 1399986792 +0200 pull: fast-forward +933655cc7d8def1beddb1f60ed576d1653ef8504 9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 Sebastian DiLorenzo 1399986845 +0200 update by push +9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 e244c2ac30341cbf8f109cc96f7661258e9baa93 Sebastian DiLorenzo 1400058009 +0200 pull: fast-forward +e244c2ac30341cbf8f109cc96f7661258e9baa93 90e8ee38aac7ead43935bd7034bd4f11f91d19c4 Sebastian DiLorenzo 1400059317 +0200 pull: fast-forward +90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo 1401270130 +0200 pull: fast-forward Modified: .git/refs/heads/master =================================================================== --- .git/refs/heads/master 2014-05-14 09:23:07 UTC (rev 211) +++ .git/refs/heads/master 2014-05-28 09:42:38 UTC (rev 212) @@ -1 +1 @@ -933655cc7d8def1beddb1f60ed576d1653ef8504 +6734fab24795a8c823c6a97e0131fcfe5a235107 Modified: .git/refs/remotes/origin/master =================================================================== --- .git/refs/remotes/origin/master 2014-05-14 09:23:07 UTC (rev 211) +++ .git/refs/remotes/origin/master 2014-05-28 09:42:38 UTC (rev 212) @@ -1 +1 @@ -933655cc7d8def1beddb1f60ed576d1653ef8504 +6734fab24795a8c823c6a97e0131fcfe5a235107 Modified: pkg/TAPS/R/TAPS.r =================================================================== --- pkg/TAPS/R/TAPS.r 2014-05-14 09:23:07 UTC (rev 211) +++ pkg/TAPS/R/TAPS.r 2014-05-28 09:42:38 UTC (rev 212) @@ -3973,8 +3973,13 @@ if(restart == F) { write.table(sampleDataOri[sampleDataOri$done==T,],'SampleData.csv',sep='\t',row.names=F) + } + + if (restart == T ) { + write.table(do.call(rbind,copyNumbers), 'SampleData.csv',sep='\t',row.names=F,append=F,col.names= T) + } else { + write.table(do.call(rbind,copyNumbers), 'SampleData.csv',sep='\t',row.names=F,append=append,col.names= !append) } - write.table(do.call(rbind,copyNumbers), 'SampleData.csv',sep='\t',row.names=F,append=append,col.names= !append) }