From noreply at r-forge.r-project.org Mon Apr 28 15:41:47 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 28 Apr 2014 15:41:47 +0200 (CEST) Subject: [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 Message-ID: <20140428134147.47D8C1846A6@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 1395307680 +0100 commit: Big upgrades to homepage and genelist 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 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 1395307680 +0100 commit: Big upgrades to homepage and genelist 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 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 1395307764 +0100 pull: fast-forward 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 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