[Patchwork-commits] r214 - .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: 2014-09-04 14:07:32 +0200 (Thu, 04 Sep 2014)
New Revision: 214

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.smoothing.r
Log:
bugfix mean/median smoothing

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

Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD	2014-09-01 09:13:50 UTC (rev 213)
+++ .git/logs/HEAD	2014-09-04 12:07:32 UTC (rev 214)
@@ -96,3 +96,4 @@
 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
+cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409832387 +0200	pull: Fast-forward

Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master	2014-09-01 09:13:50 UTC (rev 213)
+++ .git/logs/refs/heads/master	2014-09-04 12:07:32 UTC (rev 214)
@@ -96,3 +96,4 @@
 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
+cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1409832387 +0200	pull: Fast-forward

Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master	2014-09-01 09:13:50 UTC (rev 213)
+++ .git/logs/refs/remotes/origin/master	2014-09-04 12:07:32 UTC (rev 214)
@@ -93,3 +93,4 @@
 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
+cefeee2662b45c7daf3b8916b967173f68b6ddcf e8cc7370da527f1d46bb81720f663ceed281e07d Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1409832387 +0200	pull: fast-forward

Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master	2014-09-01 09:13:50 UTC (rev 213)
+++ .git/refs/heads/master	2014-09-04 12:07:32 UTC (rev 214)
@@ -1 +1 @@
-cefeee2662b45c7daf3b8916b967173f68b6ddcf
+e8cc7370da527f1d46bb81720f663ceed281e07d

Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master	2014-09-01 09:13:50 UTC (rev 213)
+++ .git/refs/remotes/origin/master	2014-09-04 12:07:32 UTC (rev 214)
@@ -1 +1 @@
-cefeee2662b45c7daf3b8916b967173f68b6ddcf
+e8cc7370da527f1d46bb81720f663ceed281e07d

Modified: pkg/patchwork/R/patchwork.smoothing.r
===================================================================
--- pkg/patchwork/R/patchwork.smoothing.r	2014-09-01 09:13:50 UTC (rev 213)
+++ pkg/patchwork/R/patchwork.smoothing.r	2014-09-04 12:07:32 UTC (rev 214)
@@ -47,8 +47,8 @@
 				j=kbposix[i]
 				#Create 50 bp windows to take median coverage of for tumor and normal/reference
 				ix <- (j-(window/2)):(j+(window/2))
-				coverage[i] <- mean(norm[ix], na.rm=T)
-				refcoverage[i] <- mean(reference[ix], na.rm=T)
+				coverage[i] <- median(norm[ix], na.rm=T)
+				refcoverage[i] <- median(reference[ix], na.rm=T)
 				}
 			kbsegs <- rbind(kbsegs,data.frame('chr'=c,kbpos,coverage,refcoverage))
 			}