[Patchwork-commits] r213 - .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
Mon Sep 1 11:13:50 CEST 2014
Author: sebastian_d
Date: 2014-09-01 11:13:50 +0200 (Mon, 01 Sep 2014)
New Revision: 213
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
pkg/TAPS/R/sysdata.rda
Log:
Added Y chrom to TAPS plots, bug fixes.
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2014-05-28 09:42:38 UTC (rev 212)
+++ .git/logs/HEAD 2014-09-01 09:13:50 UTC (rev 213)
@@ -95,3 +95,4 @@
9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 e244c2ac30341cbf8f109cc96f7661258e9baa93 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1400058009 +0200 pull: Fast-forward
e244c2ac30341cbf8f109cc96f7661258e9baa93 90e8ee38aac7ead43935bd7034bd4f11f91d19c4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1400059317 +0200 pull: Fast-forward
90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1401270131 +0200 pull: Fast-forward
+6734fab24795a8c823c6a97e0131fcfe5a235107 cefeee2662b45c7daf3b8916b967173f68b6ddcf Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409562736 +0200 pull: Fast-forward
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2014-05-28 09:42:38 UTC (rev 212)
+++ .git/logs/refs/heads/master 2014-09-01 09:13:50 UTC (rev 213)
@@ -95,3 +95,4 @@
9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 e244c2ac30341cbf8f109cc96f7661258e9baa93 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1400058009 +0200 pull: Fast-forward
e244c2ac30341cbf8f109cc96f7661258e9baa93 90e8ee38aac7ead43935bd7034bd4f11f91d19c4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1400059317 +0200 pull: Fast-forward
90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1401270131 +0200 pull: Fast-forward
+6734fab24795a8c823c6a97e0131fcfe5a235107 cefeee2662b45c7daf3b8916b967173f68b6ddcf Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409562736 +0200 pull: Fast-forward
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2014-05-28 09:42:38 UTC (rev 212)
+++ .git/logs/refs/remotes/origin/master 2014-09-01 09:13:50 UTC (rev 213)
@@ -92,3 +92,4 @@
9c0a6e3ae1d10f0d2e8e565600b7b86eb13b9518 e244c2ac30341cbf8f109cc96f7661258e9baa93 Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1400058009 +0200 pull: fast-forward
e244c2ac30341cbf8f109cc96f7661258e9baa93 90e8ee38aac7ead43935bd7034bd4f11f91d19c4 Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1400059317 +0200 pull: fast-forward
90e8ee38aac7ead43935bd7034bd4f11f91d19c4 6734fab24795a8c823c6a97e0131fcfe5a235107 Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1401270130 +0200 pull: fast-forward
+6734fab24795a8c823c6a97e0131fcfe5a235107 cefeee2662b45c7daf3b8916b967173f68b6ddcf Sebastian DiLorenzo <S_D at Sebastians-iMac.local> 1409562735 +0200 pull: fast-forward
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2014-05-28 09:42:38 UTC (rev 212)
+++ .git/refs/heads/master 2014-09-01 09:13:50 UTC (rev 213)
@@ -1 +1 @@
-6734fab24795a8c823c6a97e0131fcfe5a235107
+cefeee2662b45c7daf3b8916b967173f68b6ddcf
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2014-05-28 09:42:38 UTC (rev 212)
+++ .git/refs/remotes/origin/master 2014-09-01 09:13:50 UTC (rev 213)
@@ -1 +1 @@
-6734fab24795a8c823c6a97e0131fcfe5a235107
+cefeee2662b45c7daf3b8916b967173f68b6ddcf
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2014-05-28 09:42:38 UTC (rev 212)
+++ pkg/TAPS/R/TAPS.r 2014-09-01 09:13:50 UTC (rev 213)
@@ -293,7 +293,7 @@
sampleData=load.txt('SampleData.csv')
}
- if (length(grep('SampleData.csv',dir()))==1)
+ if (length(grep('SampleData.csv$',dir()))==1)
{
sampleData=load.txt('SampleData.csv')
} else
@@ -1123,9 +1123,9 @@
### beräkna tumorcellshalt!!
# Mha modellparameter
- ## empirical delta for whole copy: 0.55
+ ## empirical delta-R for ±one copy in diploid sample: 0.63 for Cyto/SNP6 and 0.48 for Illu
model$k2=model$k*model$meanCn
- model$tumorDNA_fromLogR=(model$k*model$meanCn)/0.55
+ model$tumorDNA_fromLogR=model$k2/0.63
model$tumorCell_fromLogR=1/ (1+model$meanCn/2* (1/model$tumorDNA_fromLogR -1))
# Mha SNPs
@@ -1932,8 +1932,8 @@
bottom=c(rep(2*(0.75/3)+0.15,8),rep((0.75/3)+0.15,8),rep(0.15,8)),
top=c(rep(0.9,8),rep(2*(0.75/3)+0.15,8),rep((0.75/3)+0.15,8)))),1) #screen 1 becomes screen 3 - 26
- split.screen(as.matrix(data.frame(left=c(rep(0.05,3)),
- right=c(rep(1,3)),
+ split.screen(as.matrix(data.frame(left=c(rep(0.015,3)),
+ right=c(rep(0.987,3)),
bottom=c(0.15,0.5,0.55),
top=c(0.5,0.55,1))),2) #screen 2 become screen 27-29
@@ -1959,7 +1959,7 @@
#nchr=24; if (sum(chr=='chrY')==0) nchr=23
#Loop over and plot the 24 chromosomes
- for (c in 1:23)
+ for (c in 1:24)
{
#Pick a chromosome
this <- chroms[chroms$c==c,]
@@ -2053,12 +2053,13 @@
par(lend=1)
#Remove chrY,M,XY
- mval[mchr=='chrY'|mchr=='chrXY'|mchr=='chrM']=NA
+ mval[mchr=='chrXY'|mchr=='chrM']=NA
+ # mval[mchr=='chrY'|mchr=='chrXY'|mchr=='chrM']=NA
#Calculate previous distance of whole genome so the next chromsome is added
#at the correct coordinate
- pre=rep(NA,23)
- for (c in 1:23)
+ pre=rep(NA,24)
+ for (c in 1:24)
{
this <- chroms[chroms$c==c,]
ix <- chr==as.character(this$chr)
@@ -2118,7 +2119,7 @@
col = '#00000003',
xaxt="n",
axes=F,
- ylim = c(ymin,ymax),
+ ylim = c(-2,2),
xlim = c(0,max(mpos))
)
@@ -2135,7 +2136,7 @@
lwd=1)
#Add colored segment information for each chromosome, red to blue gradient.
- for(c in 1:23)
+ for(c in 1:24)
{
this <- chroms[chroms$c==c,]
ix <- chr==as.character(this$chr)
@@ -2210,7 +2211,7 @@
par(mgp =c(1,0.5,0))
#Remove chrY,M,XY
- sval[mchr=='chrY'|mchr=='chrXY'|mchr=='chrM']=NA
+ sval[mchr=='chrXY'|mchr=='chrM']=NA
#Index to avoid spos/sval values that are all the way at 0 or 1.
ix = !(sval %in% c(0,1))
@@ -2232,7 +2233,7 @@
#Add axis to the left,right and below of AI. The below axis is the chromosome numbers 1-24.
axis(side=2,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=0,las=1)
- axis(side=1,at=pre,pos=0,labels=c(seq(from=1,to=22),"X"),cex.axis=0.55,lty=0)#,tck=0,col.ticks='#00000000')
+ axis(side=1,at=pre,pos=0,labels=c(seq(from=1,to=22),"X",'Y'),cex.axis=0.55,lty=0)#,tck=0,col.ticks='#00000000')
axis(side=4,tck=-0.04,at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=max(mpos),las=1) #
mtext("Allele frequency",side=2,line=0)
mtext("Chromosomes",side=1,line=1.5,adj=0.4)
@@ -2304,7 +2305,7 @@
#size[length>10000000]=4
#Loop over each chromosome. (Not chromosomeY as of writing)
- for (c in 1:23)
+ for (c in 1:24)
{
#Select the chromosome
@@ -2375,8 +2376,7 @@
col = c(col[notix],col[ix]),
xlim = xlim,
ylim = ylim)
- }
- else
+ } else
{
plot(int[notix],ai[notix],
pch=16,
@@ -2394,8 +2394,7 @@
if(c!=23)
{
points(int[xix],ai[xix],pch=4,cex=0.5,col='#46464620')
- }
- else
+ } else
{
points(int[xix],ai[xix],pch=4,cex=0.5,col=col[ix])
}
@@ -3804,7 +3803,7 @@
close <- F
write.table(x=rbind(colnames(newSampleData)),file=paste(root,'backup.csv',sep='/'),sep='\t',row.names=F,col.names=F)
- if(nrow(sampleDataOri[sampleDataOri$done==T]) > 0) {
+ if(nrow(sampleDataOri[sampleDataOri$done==T,]) > 0) {
write.table(x=sampleDataOri[sampleDataOri$done==T,],file=paste(root,'backup.csv',sep='/'),sep='\t',row.names=F,col.names=F,append=T)
}
Modified: pkg/TAPS/R/sysdata.rda
===================================================================
(Binary files differ)
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