[Patchwork-commits] r206 - .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]

Author: sebastian_d
Date: 2014-04-28 15:41:46 +0200 (Mon, 28 Apr 2014)
New Revision: 206

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:
buggfix markus taps_compare

Modified: .git/index
===================================================================
(Binary files differ)

Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD	2014-03-26 10:37:57 UTC (rev 205)
+++ .git/logs/HEAD	2014-04-28 13:41:46 UTC (rev 206)
@@ -87,3 +87,4 @@
 0fc6463401c39565b48199c6f4adfe077510620e 53a860b490c7ac5501d8bb4f6b95e700491e12d4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395307680 +0100	commit: Big upgrades to homepage and genelist
 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

Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master	2014-03-26 10:37:57 UTC (rev 205)
+++ .git/logs/refs/heads/master	2014-04-28 13:41:46 UTC (rev 206)
@@ -87,3 +87,4 @@
 0fc6463401c39565b48199c6f4adfe077510620e 53a860b490c7ac5501d8bb4f6b95e700491e12d4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395307680 +0100	commit: Big upgrades to homepage and genelist
 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

Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master	2014-03-26 10:37:57 UTC (rev 205)
+++ .git/logs/refs/remotes/origin/master	2014-04-28 13:41:46 UTC (rev 206)
@@ -84,3 +84,4 @@
 0fc6463401c39565b48199c6f4adfe077510620e bf30fc707ee93417a8fad1f8ab1d8dc7426e128a Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1395307764 +0100	pull: fast-forward
 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

Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master	2014-03-26 10:37:57 UTC (rev 205)
+++ .git/refs/heads/master	2014-04-28 13:41:46 UTC (rev 206)
@@ -1 +1 @@
-79c9a62cd0b934e0f252e2fb660c26ffeeeea825
+cb2b4bc53aac68ec1b56532dbbded71b4eca7582

Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master	2014-03-26 10:37:57 UTC (rev 205)
+++ .git/refs/remotes/origin/master	2014-04-28 13:41:46 UTC (rev 206)
@@ -1 +1 @@
-79c9a62cd0b934e0f252e2fb660c26ffeeeea825
+cb2b4bc53aac68ec1b56532dbbded71b4eca7582

Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r	2014-03-26 10:37:57 UTC (rev 205)
+++ pkg/TAPS/R/TAPS.r	2014-04-28 13:41:46 UTC (rev 206)
@@ -1467,7 +1467,6 @@
 ### Markus 2013.
 ### Function for summarizing alteration frquencies in X samples
 TAPS_freq <- function(samples='all', outdir='frequencies', hg19=T) {
-    
     #suppressPackageStartupMessages(library(xlsx))    
     
     sampleData <- load.txt('SampleData.csv')
@@ -1500,14 +1499,15 @@
         table$meanCn <- meanCns[i] <- round(weightedMean(table$Cn_[ix], table$lengthMB[ix]),2)    
         samples <- rbind(samples,table) 
     }
+
+    samples=samples[!is.na(samples$Cn),]
+    regs=samples[samples$Chromosome!='chrY',]
     
-    samples=samples[samples$Chromosome!='chrY',]
-    
     if (hg19) genes <- knownGene else genes <- knownGene_hg18
     genes$name2=genes$gAlias
     genes$chrom=genes$chr
     
-    regs=samples
+    
     n=length(unique(regs$name))
     
     gaincolor='#007602'
@@ -1630,7 +1630,7 @@
 
 ########### Group comparisons
 TAPS_compare <- function(grp1, grp2, name1='1', name2='2', outdir='frequencies_comp', hg19=T) {
-    
+
     #suppressPackageStartupMessages(library(xlsx))    
 
     sampleData=load.txt('SampleData.csv')
@@ -1662,14 +1662,15 @@
     nSamples=length(grps)
     
     for (i in 1:nSamples) {
-        table <- load.txt(paste(olddir,'/',subs[i],'/',subs[i],'_segmentCN.txt',sep=''))
+        table <- load.txt(paste(olddir,'/',grps[i],'/',grps[i],'_segmentCN.txt',sep=''))
         table$n <- i
-        table$name <- as.character(subs[i])    
+        table$name <- as.character(grps[i])    
         ix <- as.numeric(deChrom_ucsc(table$Chromosome)) <= 22
         table$meanCn <- meanCns[i] <- round(weightedMean(table$Cn_[ix], table$lengthMB[ix]),2)    
         samples <- rbind(samples,table) 
     }
     
+    samples=samples[!is.na(samples$Cn),]
     samples=samples[samples$Chromosome!='chrY',]
     
     if (hg19) genes <- knownGene else genes <- knownGene_hg18
@@ -1723,7 +1724,6 @@
                               comparison='', 
                               name1='1', name2='2', 
                               color='#000000') {    
-
     p_cutoff <- 0.05
     freq_cutoff <- 0