[Patchwork-commits] r217 - .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
Fri Jun 26 09:33:33 CEST 2015
Author: sebastian_d
Date: 2015-06-26 09:33:33 +0200 (Fri, 26 Jun 2015)
New Revision: 217
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:
TAPS update markus
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2015-06-18 08:25:41 UTC (rev 216)
+++ .git/logs/HEAD 2015-06-26 07:33:33 UTC (rev 217)
@@ -99,3 +99,4 @@
cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409832387 +0200 pull: Fast-forward
e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1411979666 +0200 pull: Fast-forward
b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615906 +0200 pull: Fast-forward
+52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200 pull: Fast-forward
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2015-06-18 08:25:41 UTC (rev 216)
+++ .git/logs/refs/heads/master 2015-06-26 07:33:33 UTC (rev 217)
@@ -99,3 +99,4 @@
cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409832387 +0200 pull: Fast-forward
e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1411979666 +0200 pull: Fast-forward
b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615906 +0200 pull: Fast-forward
+52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200 pull: Fast-forward
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2015-06-18 08:25:41 UTC (rev 216)
+++ .git/logs/refs/remotes/origin/master 2015-06-26 07:33:33 UTC (rev 217)
@@ -96,3 +96,4 @@
cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1409832387 +0200 pull: fast-forward
e8cc7370da527f1d46bb81720f663ceed281e07d b5798bb1874d9dc8e50fa5083961a8836d79f76c Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1411979666 +0200 pull: fast-forward
b5798bb1874d9dc8e50fa5083961a8836d79f76c 52402622419759bc3642b6f49dd0f4abd2003d38 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1434615905 +0200 pull: fast-forward
+52402622419759bc3642b6f49dd0f4abd2003d38 4bbde19cc8582ba3fb6caf01b1b01165c5db15d6 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1435303966 +0200 pull: fast-forward
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2015-06-18 08:25:41 UTC (rev 216)
+++ .git/refs/heads/master 2015-06-26 07:33:33 UTC (rev 217)
@@ -1 +1 @@
-52402622419759bc3642b6f49dd0f4abd2003d38
+4bbde19cc8582ba3fb6caf01b1b01165c5db15d6
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2015-06-18 08:25:41 UTC (rev 216)
+++ .git/refs/remotes/origin/master 2015-06-26 07:33:33 UTC (rev 217)
@@ -1 +1 @@
-52402622419759bc3642b6f49dd0f4abd2003d38
+4bbde19cc8582ba3fb6caf01b1b01165c5db15d6
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2015-06-18 08:25:41 UTC (rev 216)
+++ pkg/TAPS/R/TAPS.r 2015-06-26 07:33:33 UTC (rev 217)
@@ -15,6 +15,7 @@
TAPS_plot <- function(#samples='all',
directory=NULL,autoEstimate=FALSE,
bin=250,cores=1,matched=FALSE,allelePeaks=FALSE) {
+ cores=1
#Automatically check, and if needed install, packages stats and fields
#Load stats. It should be in all, at least semi-new, R distributions so we dont need to install.package it or
@@ -155,10 +156,12 @@
Log2=Log2[!is.nan(Log2$Value),]
Log2=Log2[!is.na(Log2$Value),]
Log2 <- Log2[which(Log2$Value != -Inf & Log2$Value != +Inf ),]
+ Log2=chromFix(Log2)
alf=alf[!is.nan(alf$Value),]
alf=alf[!is.na(alf$Value),]
alf$Value[alf$Value<0]=0; alf$Value[alf$Value>1]=1
alf <- alf[which(alf$Value != -Inf & alf$Value != +Inf ),]
+ alf=chromFix(alf)
segments <- readSegments() ## segments if available (CBS recommended)
@@ -266,6 +269,7 @@
###
TAPS_call <- function(samples='all',directory=getwd(),cores=1) {
+ cores=1
minseg=1
maxCn=12
#suppressPackageStartupMessages(library(xlsx))
@@ -330,20 +334,32 @@
# cat(' ..loading', subs[i])
print(paste(i,'/',length(subs),': ',subs[i],' Loading',sep=''))
- Log2 <- readLog2()
- alf <- readAlf(localDir)
+ if (file.exists('rawcopy.Rdata')) {
+ load('rawcopy.Rdata')
+ Log2=probes.txt[,2:5]
+ alf=snps.txt[,2:5]
+ } else {
+ Log2 <- readLog2()
+ alf <- readAlf(localDir)
+ }
segments <- readSegments()
#Some samples contain NA values, we simply remove these.
Log2=Log2[!is.nan(Log2$Value),]
+ Log2=chromFix(Log2)
+
Log2=Log2[!is.na(Log2$Value),]
alf=alf[!is.nan(alf$Value),]
alf=alf[!is.na(alf$Value),]
+ alf=chromFix(alf)
+
segments <- segments[!is.nan(segments$Value),]
segments <- segments[!is.na(segments$Value),]
+ segments=chromFix(segments)
+
segments$Value <- segments$Value-mean(Log2$Value)
Log2$Value <- Log2$Value-mean(Log2$Value)
@@ -1533,7 +1549,7 @@
### Function for summarizing alteration frquencies in X samples
TAPS_freq <- function(samples='all', outdir='frequencies', hg19=T) {
#suppressPackageStartupMessages(library(xlsx))
-
+ #browser()
sampleData <- load.txt('SampleData.csv')
olddir <- getwd()
if (!is.na(outdir)) {
@@ -1556,14 +1572,17 @@
## Load and parse all samples
samples <- meanCns <- NULL
- for (i in 1:nSamples) {
+ for (i in 1:nSamples) try( {
+ #cat(subs[i],'\n')
table <- load.txt(paste(olddir,'/',subs[i],'/',subs[i],'_segmentCN.txt',sep=''))
table$n <- i
table$name <- as.character(subs[i])
ix <- as.numeric(deChrom_ucsc(table$Chromosome)) <= 22
+ table=table[!is.na(ix),]
+ ix <- as.numeric(deChrom_ucsc(table$Chromosome)) <= 22
table$meanCn <- meanCns[i] <- round(weightedMean(table$Cn_[ix], table$lengthMB[ix]),2)
samples <- rbind(samples,table)
- }
+ }, silent=T)
samples=samples[!is.na(samples$Cn),]
regs=samples[samples$Chromosome!='chrY',]
@@ -4056,3 +4075,8 @@
}
+chromFix <- function(data) {
+ if (any(data$Chromosome=='1'))
+ data$Chromosome=paste('chr',data$Chromosome,sep='')
+ return(data)
+}
\ No newline at end of file
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