[Patchwork-commits] r165 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2013-03-15 14:47:20 +0100 (Fri, 15 Mar 2013)
New Revision: 165

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/patchwork/R/patchwork.alleledata.r
   pkg/patchwork/R/patchwork.plot.r
Log:
Hopefully fixed a bugg where AI got set to 0 for all snps

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

Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD	2013-03-12 13:34:03 UTC (rev 164)
+++ .git/logs/HEAD	2013-03-15 13:47:20 UTC (rev 165)
@@ -34,3 +34,5 @@
 ae581e53647259304439e470cd67db340b07cb35 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1361523526 +0100	commit: some homepage updates from alexeys feedback
 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d 5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363092610 +0100	commit: Add titles to patchwork plots among other things
 5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 6a55102231aa819f1e4616dde7c28ea32af8a06c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363095404 +0100	pull : Fast-forward
+6a55102231aa819f1e4616dde7c28ea32af8a06c 22eb0c8de456d9ed783868a3db491b52008fb116 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363252090 +0100	pull : Fast-forward
+22eb0c8de456d9ed783868a3db491b52008fb116 028901af11a1b01a4147feab3f19214457984911 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363350024 +0100	pull : Fast-forward

Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master	2013-03-12 13:34:03 UTC (rev 164)
+++ .git/logs/refs/heads/master	2013-03-15 13:47:20 UTC (rev 165)
@@ -34,3 +34,5 @@
 ae581e53647259304439e470cd67db340b07cb35 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1361523526 +0100	commit: some homepage updates from alexeys feedback
 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d 5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363092610 +0100	commit: Add titles to patchwork plots among other things
 5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 6a55102231aa819f1e4616dde7c28ea32af8a06c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363095404 +0100	pull : Fast-forward
+6a55102231aa819f1e4616dde7c28ea32af8a06c 22eb0c8de456d9ed783868a3db491b52008fb116 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363252090 +0100	pull : Fast-forward
+22eb0c8de456d9ed783868a3db491b52008fb116 028901af11a1b01a4147feab3f19214457984911 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363350024 +0100	pull : Fast-forward

Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master	2013-03-12 13:34:03 UTC (rev 164)
+++ .git/logs/refs/remotes/origin/master	2013-03-15 13:47:20 UTC (rev 165)
@@ -34,3 +34,5 @@
 ae581e53647259304439e470cd67db340b07cb35 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1361523599 +0100	update by push
 2fdc7676c81d53b78e022a0f9d97b06c7133fc0d 5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363092633 +0100	update by push
 5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 6a55102231aa819f1e4616dde7c28ea32af8a06c Sebastian DiLorenzo <S_D at imv071.medsci.uu.se> 1363095404 +0100	pull : fast-forward
+6a55102231aa819f1e4616dde7c28ea32af8a06c 22eb0c8de456d9ed783868a3db491b52008fb116 Sebastian DiLorenzo <S_D at imv071.medsci.uu.se> 1363252090 +0100	pull : fast-forward
+22eb0c8de456d9ed783868a3db491b52008fb116 028901af11a1b01a4147feab3f19214457984911 Sebastian DiLorenzo <S_D at imv071.medsci.uu.se> 1363350024 +0100	pull : fast-forward

Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master	2013-03-12 13:34:03 UTC (rev 164)
+++ .git/refs/heads/master	2013-03-15 13:47:20 UTC (rev 165)
@@ -1 +1 @@
-6a55102231aa819f1e4616dde7c28ea32af8a06c
+028901af11a1b01a4147feab3f19214457984911

Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master	2013-03-12 13:34:03 UTC (rev 164)
+++ .git/refs/remotes/origin/master	2013-03-15 13:47:20 UTC (rev 165)
@@ -1 +1 @@
-6a55102231aa819f1e4616dde7c28ea32af8a06c
+028901af11a1b01a4147feab3f19214457984911

Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r	2013-03-12 13:34:03 UTC (rev 164)
+++ pkg/patchwork/R/patchwork.alleledata.r	2013-03-15 13:47:20 UTC (rev 165)
@@ -82,7 +82,7 @@
 
 	# Annotate with dbSNP
 	dbSnp=dbSnp[,c(1,3)]; dbSnp$dbSnp=T
-	alf=merge(alf,dbSnp[,c(1,3)], all.x=T, all.y=F, by=1:2)
+	alf=merge(alf,dbSnp, all.x=T, all.y=F, by=1:2)
 	alf$dbSnp[is.na(alf$dbSnp)]=F
 
 	#Finally, if a matched normal was available, remove SNPs that were not (somewhat) heterozygous there.

Modified: pkg/patchwork/R/patchwork.plot.r
===================================================================
--- pkg/patchwork/R/patchwork.plot.r	2013-03-12 13:34:03 UTC (rev 164)
+++ pkg/patchwork/R/patchwork.plot.r	2013-03-15 13:47:20 UTC (rev 165)
@@ -73,9 +73,9 @@
 			normalalf <- normalalf[normalalf$amin/normalalf$atot > 0.2,]
 			alf <- merge(normalalf[,1:2],alf,by=1:2,all=F)
 			} else 
-			{ ## If there is NO pileup for matched normal
-				alf <- alf[alf$dbSnp==T,]
-				alf <- alf[alf$min>1 & alf$ref>2,]
+			{ ## If there was NO pileup for matched normal
+			alf <- alf[alf$dbSnp==T,]
+			alf <- alf[alf$amin>1 & alf$aref>2,]
 			}