Mercurial > repos > jfb > kinatest_7_7

changeset 6:891f465be772 draft

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Uploaded
author jfb
date Wed, 28 Feb 2018 11:01:21 -0500
parents d5e964823147
children 231e41a2d167
files kinatestid_r/Kinatest-R.R kinatestid_r/kinatestid_r.xml
diffstat 2 files changed, 43 insertions(+), 43 deletions(-) [+]
line wrap: on
line diff
--- a/kinatestid_r/Kinatest-R.R	Wed Feb 28 10:53:29 2018 -0500
+++ b/kinatestid_r/Kinatest-R.R	Wed Feb 28 11:01:21 2018 -0500
@@ -1153,6 +1153,40 @@
 bareSDs<-SDtable[2:21,2:16]
 goodones<-bareSDs>2
 
+# Positionm7<-which(goodones[,1] %in% TRUE)
+# if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
+# Positionm6<-which(goodones[,2] %in% TRUE)
+# if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
+# Positionm5<-which(goodones[,3] %in% TRUE)
+# if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
+# Positionm4<-which(goodones[,4] %in% TRUE)
+# if (length(Positionm4)<2){Positionm4<-bareSDs[,4][order(bareSDs[,4])[1:2]]}
+# Positionm3<-which(goodones[,5] %in% TRUE)
+# if (length(Positionm3)<2){Positionm3<-bareSDs[,5][order(bareSDs[,5])[1:2]]}
+# Positionm2<-which(goodones[,6] %in% TRUE)
+# if (length(Positionm2)<2){Positionm2<-bareSDs[,6][order(bareSDs[,6])[1:2]]}
+# Positionm1<-which(goodones[,7] %in% TRUE)
+# if (length(Positionm1)<2){Positionm1<-bareSDs[,7][order(bareSDs[,7])[1:2]]}
+# 
+# Positiond0<-which(goodones[,8] %in% TRUE)
+# if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
+# 
+# Positionp1<-which(goodones[,9] %in% TRUE)
+# if (length(Positionp1)<2){Positionp1<-bareSDs[,9][order(bareSDs[,9])[1:2]]}
+# Positionp2<-which(goodones[,10] %in% TRUE)
+# if (length(Positionp2)<2){Positionp2<-bareSDs[,10][order(bareSDs[,10])[1:2]]}
+# Positionp3<-which(goodones[,11] %in% TRUE)
+# if (length(Positionp3)<2){Positionp3<-bareSDs[,11][order(bareSDs[,11])[1:2]]}
+# Positionp4<-which(goodones[,12] %in% TRUE)
+# if (length(Positionp4)<2){Positionp4<-bareSDs[,12][order(bareSDs[,12])[1:2]]}
+# Positionp5<-which(goodones[,13] %in% TRUE)
+# if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
+# Positionp6<-which(goodones[,14] %in% TRUE)
+# if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
+# Positionp7<-which(goodones[,15] %in% TRUE)
+# if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
+
+
 Positionm7<-which(goodones[,1] %in% TRUE)
 if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
 Positionm6<-which(goodones[,2] %in% TRUE)
@@ -1160,25 +1194,25 @@
 Positionm5<-which(goodones[,3] %in% TRUE)
 if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
 Positionm4<-which(goodones[,4] %in% TRUE)
-if (length(Positionm4)<2){Positionm4<-bareSDs[,4][order(bareSDs[,4])[1:2]]}
+if (length(Positionm4)<1){Positionm4<-which(bareSDs[,4]==max(bareSDs[,4]))}
 Positionm3<-which(goodones[,5] %in% TRUE)
-if (length(Positionm3)<2){Positionm3<-bareSDs[,5][order(bareSDs[,5])[1:2]]}
+if (length(Positionm3)<1){Positionm3<-which(bareSDs[,5]==max(bareSDs[,5]))}
 Positionm2<-which(goodones[,6] %in% TRUE)
-if (length(Positionm2)<2){Positionm2<-bareSDs[,6][order(bareSDs[,6])[1:2]]}
+if (length(Positionm2)<1){Positionm2<-which(bareSDs[,6]==max(bareSDs[,6]))}
 Positionm1<-which(goodones[,7] %in% TRUE)
-if (length(Positionm1)<2){Positionm1<-bareSDs[,7][order(bareSDs[,7])[1:2]]}
+if (length(Positionm1)<1){Positionm1<-which(bareSDs[,7]==max(bareSDs[,7]))}
 
 Positiond0<-which(goodones[,8] %in% TRUE)
 if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
 
 Positionp1<-which(goodones[,9] %in% TRUE)
-if (length(Positionp1)<2){Positionp1<-bareSDs[,9][order(bareSDs[,9])[1:2]]}
+if (length(Positionp1)<1){Positionp1<-which(bareSDs[,9]==max(bareSDs[,9]))}
 Positionp2<-which(goodones[,10] %in% TRUE)
-if (length(Positionp2)<2){Positionp2<-bareSDs[,10][order(bareSDs[,10])[1:2]]}
+if (length(Positionp2)<1){Positionp2<-which(bareSDs[,10]==max(bareSDs[,10]))}
 Positionp3<-which(goodones[,11] %in% TRUE)
-if (length(Positionp3)<2){Positionp3<-bareSDs[,11][order(bareSDs[,11])[1:2]]}
+if (length(Positionp3)<1){Positionp3<-which(bareSDs[,11]==max(bareSDs[,11]))}
 Positionp4<-which(goodones[,12] %in% TRUE)
-if (length(Positionp4)<2){Positionp4<-bareSDs[,12][order(bareSDs[,12])[1:2]]}
+if (length(Positionp4)<1){Positionp4<-which(bareSDs[,12]==max(bareSDs[,12]))}
 Positionp5<-which(goodones[,13] %in% TRUE)
 if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
 Positionp6<-which(goodones[,14] %in% TRUE)
@@ -1186,40 +1220,6 @@
 Positionp7<-which(goodones[,15] %in% TRUE)
 if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
 
-
-# Positionm7<-which(goodones[,1] %in% TRUE)
-# if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
-# Positionm6<-which(goodones[,2] %in% TRUE)
-# if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
-# Positionm5<-which(goodones[,3] %in% TRUE)
-# if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
-# Positionm4<-which(goodones[,4] %in% TRUE)
-# if (length(Positionm4)<1){Positionm4<-which(bareSDs[,4]==max(bareSDs[,4]))}
-# Positionm3<-which(goodones[,5] %in% TRUE)
-# if (length(Positionm3)<1){Positionm3<-which(bareSDs[,5]==max(bareSDs[,5]))}
-# Positionm2<-which(goodones[,6] %in% TRUE)
-# if (length(Positionm2)<1){Positionm2<-which(bareSDs[,6]==max(bareSDs[,6]))}
-# Positionm1<-which(goodones[,7] %in% TRUE)
-# if (length(Positionm1)<1){Positionm1<-which(bareSDs[,7]==max(bareSDs[,7]))}
-# 
-# Positiond0<-which(goodones[,8] %in% TRUE)
-# if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
-# 
-# Positionp1<-which(goodones[,9] %in% TRUE)
-# if (length(Positionp1)<1){Positionp1<-which(bareSDs[,9]==max(bareSDs[,9]))}
-# Positionp2<-which(goodones[,10] %in% TRUE)
-# if (length(Positionp2)<1){Positionp2<-which(bareSDs[,10]==max(bareSDs[,10]))}
-# Positionp3<-which(goodones[,11] %in% TRUE)
-# if (length(Positionp3)<1){Positionp3<-which(bareSDs[,11]==max(bareSDs[,11]))}
-# Positionp4<-which(goodones[,12] %in% TRUE)
-# if (length(Positionp4)<1){Positionp4<-which(bareSDs[,12]==max(bareSDs[,12]))}
-# Positionp5<-which(goodones[,13] %in% TRUE)
-# if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
-# Positionp6<-which(goodones[,14] %in% TRUE)
-# if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
-# Positionp7<-which(goodones[,15] %in% TRUE)
-# if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
-
 # Positionm7<-which(goodones[,1] %in% TRUE)
 # if (length(Positionm7)<3){Positionm7<-bareSDs[,1][order(bareSDs[,1])[1:3]]}
 # Positionm6<-which(goodones[,2] %in% TRUE)
--- a/kinatestid_r/kinatestid_r.xml	Wed Feb 28 10:53:29 2018 -0500
+++ b/kinatestid_r/kinatestid_r.xml	Wed Feb 28 11:01:21 2018 -0500
@@ -40,7 +40,7 @@
 Important!
 **Please write the name of your kinase in ALL CAPS so the R script can recognize it!  Thank you!**
 **If your kinase is one of the following kinases, please use this form of its name:  ABL, ARG, BTK, CSK, FYN, HCK, JAK2, LCK, LYN, PYK2, SRC, SYK, YES, FLT3**
-**So for example if your kinase is ARG please use ARG and not ABL2
+**So for example if your kinase is ARG please use ARG and not ABL2**
 	
 This tool is intended for use in conjunction with KinaMine.jar and Negative Motif Finder.  Using the outputs from those two functions (The Positive and Negative substrates as well as the Substrate Background Frequency) this tool calculates optimal substrates