[Patchwork-commits] r179 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/TAPS/R www/css/img
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jun 25 14:16:17 CEST 2013
Author: sebastian_d
Date: 2013-06-25 14:16:16 +0200 (Tue, 25 Jun 2013)
New Revision: 179
Added:
www/css/img/Chas.png
www/css/img/Main_folder.png
www/css/img/Nexus.png
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:
Add some picture files for taps that i forgot
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-06-24 12:33:05 UTC (rev 178)
+++ .git/COMMIT_EDITMSG 2013-06-25 12:16:16 UTC (rev 179)
@@ -1 +1 @@
-buggfix for mpilup and patchwork.alleledata
+added some images that i forgot
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-06-24 12:33:05 UTC (rev 178)
+++ .git/logs/HEAD 2013-06-25 12:16:16 UTC (rev 179)
@@ -51,3 +51,5 @@
49637041dfcf47c07ecaa49251071ba4e2ad377a 85bd8859e23a1fd9cc13dca12d161787786508c9 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371644646 +0200 commit: hopefully fixes to mpile2alleles
85bd8859e23a1fd9cc13dca12d161787786508c9 86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371719448 +0200 commit: Another fix to mpileup. Time for a QA
86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076903 +0200 commit: small change to alleledata to fix HG check.
+5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 998b2f7c44be9ba4a1a31c630143e4f755bf3b32 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162569 +0200 commit: added some images that i forgot
+998b2f7c44be9ba4a1a31c630143e4f755bf3b32 e557c8daaad5d3fba321242275706fa9e3138286 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162589 +0200 pull : Merge made by recursive.
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-06-24 12:33:05 UTC (rev 178)
+++ .git/logs/refs/heads/master 2013-06-25 12:16:16 UTC (rev 179)
@@ -51,3 +51,5 @@
49637041dfcf47c07ecaa49251071ba4e2ad377a 85bd8859e23a1fd9cc13dca12d161787786508c9 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371644646 +0200 commit: hopefully fixes to mpile2alleles
85bd8859e23a1fd9cc13dca12d161787786508c9 86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371719448 +0200 commit: Another fix to mpileup. Time for a QA
86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076903 +0200 commit: small change to alleledata to fix HG check.
+5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 998b2f7c44be9ba4a1a31c630143e4f755bf3b32 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162569 +0200 commit: added some images that i forgot
+998b2f7c44be9ba4a1a31c630143e4f755bf3b32 e557c8daaad5d3fba321242275706fa9e3138286 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162589 +0200 pull : Merge made by recursive.
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-06-24 12:33:05 UTC (rev 178)
+++ .git/logs/refs/remotes/origin/master 2013-06-25 12:16:16 UTC (rev 179)
@@ -49,3 +49,5 @@
49637041dfcf47c07ecaa49251071ba4e2ad377a 85bd8859e23a1fd9cc13dca12d161787786508c9 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371644659 +0200 update by push
85bd8859e23a1fd9cc13dca12d161787786508c9 86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1371719471 +0200 update by push
86dcc04de9d77c535ad155fdfd870ee62c5e9cd4 5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372076931 +0200 update by push
+5a0091d4eaca40691cb6bc59d83f9d1ab55f8566 d638a39e4e15a398cf8459744395a830bbd12287 Sebastian DiLorenzo <S_D at imv096.medsci.uu.se> 1372162589 +0200 pull : fast-forward
+d638a39e4e15a398cf8459744395a830bbd12287 e557c8daaad5d3fba321242275706fa9e3138286 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1372162603 +0200 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-06-24 12:33:05 UTC (rev 178)
+++ .git/refs/heads/master 2013-06-25 12:16:16 UTC (rev 179)
@@ -1 +1 @@
-5a0091d4eaca40691cb6bc59d83f9d1ab55f8566
+e557c8daaad5d3fba321242275706fa9e3138286
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-06-24 12:33:05 UTC (rev 178)
+++ .git/refs/remotes/origin/master 2013-06-25 12:16:16 UTC (rev 179)
@@ -1 +1 @@
-5a0091d4eaca40691cb6bc59d83f9d1ab55f8566
+e557c8daaad5d3fba321242275706fa9e3138286
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2013-06-24 12:33:05 UTC (rev 178)
+++ pkg/TAPS/R/TAPS.r 2013-06-25 12:16:16 UTC (rev 179)
@@ -140,10 +140,10 @@
segments$Value <- segments$Value-median(Log2$Value) ## Median-centering
Log2$Value <- Log2$Value-median(Log2$Value) ## Median-centering
- allRegions=NULL; #try(load('allRegions.Rdata'),silent=T)
+ allRegions=NULL; try(load('allRegions.Rdata'),silent=T)
if (is.null(allRegions)) allRegions <- makeRegions(Log2, alf, segments) ## Calculates necessary data for segments (all functions are in this file)
save(allRegions,file='allRegions.Rdata')
- regs=NULL; #try(load('shortRegions.Rdata'),silent=T)
+ regs=NULL; try(load('shortRegions.Rdata'),silent=T)
if (is.null(regs)) {
regs <- regsFromSegs(Log2,alf,segments,bin=bin,min=5) ## Calculates the same data for shortened segments
save(regs,file='shortRegions.Rdata')
@@ -151,7 +151,8 @@
## Sample QC
sampleData$MAPD[i] <- MAPD <- round(median(abs(diff(Log2$Value[Log2$Chromosome=='chr1'][order(Log2$Start[Log2$Chromosome=='chr1'])]))),2)
- sampleData$MHOF[i] <- MHOF <- round(100*median(0.5+regs$hom[regs$scores<0.5],na.rm=T),1)
+ sampleData$MHOF[i] <- MHOF <- round(100*median(0.5+abs(0.5-alf$Value)),1)
+ #round(100*median(0.5+regs$hom[regs$scores<0.5],na.rm=T),1)
#MAID=round(median(abs(diff(regs$scores[!is.na(regs$scores)]))),3)
#Save for TAPS_region()
@@ -1606,7 +1607,6 @@
#size[length>10000000]=0.8
#Define the name,dimensions and resolution of the plot.
- #pdf(paste(name,'_overview.pdf',sep=''),paper="a4r")#,width=11.7,height=8.3) #Vectorized pdf did not work well for RAM.
jpeg(paste(name,'_overview.jpg',sep=''),width=11.7,height=8.3,units="in",res=300)
#split the plot into desired formation
Added: www/css/img/Chas.png
===================================================================
(Binary files differ)
Property changes on: www/css/img/Chas.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/css/img/Main_folder.png
===================================================================
(Binary files differ)
Property changes on: www/css/img/Main_folder.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: www/css/img/Nexus.png
===================================================================
(Binary files differ)
Property changes on: www/css/img/Nexus.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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