[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
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 13 11:19:44 CEST 2014
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 <dilorenzo.sebastian at gmail.com> 1395307764 +0100 pull: Merge made by the 'recursive' strategy.
3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395830196 +0100 pull: Fast-forward
79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1398692432 +0200 pull: Fast-forward
+cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1399362996 +0200 commit: hotfix cy750K
+3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 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 <dilorenzo.sebastian at gmail.com> 1395307764 +0100 pull: Merge made by the 'recursive' strategy.
3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395830196 +0100 pull: Fast-forward
79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1398692432 +0200 pull: Fast-forward
+cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1399362996 +0200 commit: hotfix cy750K
+3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 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 <dilorenzo.sebastian at gmail.com> 1395307814 +0100 update by push
3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1395830195 +0100 pull: fast-forward
79c9a62cd0b934e0f252e2fb660c26ffeeeea825 cb2b4bc53aac68ec1b56532dbbded71b4eca7582 Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1398692432 +0200 pull: fast-forward
+cb2b4bc53aac68ec1b56532dbbded71b4eca7582 3bd7f01d1011acc7afac8a149cd922137804fd77 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1399363003 +0200 update by push
+3bd7f01d1011acc7afac8a149cd922137804fd77 18800d736527a84881558f1f00ba4af0f62807fe Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 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
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