Mercurial > repos > jfb > kinatest_r_7_7testing

comparison kinatestid_r/Kinatest-R_part2.R @ 9:f80306fc5d69 draft

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Uploaded
author jfb
date Thu, 08 Feb 2018 13:48:59 -0500
parents 2f3df9b1c05b
children
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8:927eaf73feca 9:f80306fc5d69
8 # require(rJava) 8 # require(rJava)
9 # require(xlsxjars) 9 # require(xlsxjars)
10 # require(xlsx) 10 # require(xlsx)
11 # # require(readxl) 11 # # require(readxl)
12 12
13 View(SDtable) 13 #View(SDtable)
14 bareSDs<-SDtable[2:21,2:16] 14 bareSDs<-SDtable[2:21,2:16]
15 goodones<-bareSDs>2 15 goodones<-bareSDs>2
16 16
17 Positionm7<-which(goodones[,1] %in% TRUE) 17 Positionm7<-which(goodones[,1] %in% TRUE)
18 if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))} 18 if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
47 Positionp7<-which(goodones[,15] %in% TRUE) 47 Positionp7<-which(goodones[,15] %in% TRUE)
48 if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))} 48 if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
49 49
50 aa_props2 <- c("1"="A", "2"="C", "3"="D", "4"="E", "5"="F", "6"="G", "7"="H", "8"="I", "9"="K", "10"="L", "11"="M", "12"="N", 50 aa_props2 <- c("1"="A", "2"="C", "3"="D", "4"="E", "5"="F", "6"="G", "7"="H", "8"="I", "9"="K", "10"="L", "11"="M", "12"="N",
51 "13"="P", "14"="Q", "15"="R", "16"="S", "17"="T", "18"="V", "19"="W", "20"="Y") 51 "13"="P", "14"="Q", "15"="R", "16"="S", "17"="T", "18"="V", "19"="W", "20"="Y")
52 aa_props2<-c(1="A")
53 52
54 Positionm7<-sapply(Positionm7, function (x) aa_props2[x]) 53 Positionm7<-sapply(Positionm7, function (x) aa_props2[x])
55 Positionm6<-sapply(Positionm6, function (x) aa_props2[x]) 54 Positionm6<-sapply(Positionm6, function (x) aa_props2[x])
56 Positionm5<-sapply(Positionm5, function (x) aa_props2[x]) 55 Positionm5<-sapply(Positionm5, function (x) aa_props2[x])
57 Positionm4<-sapply(Positionm4, function (x) aa_props2[x]) 56 Positionm4<-sapply(Positionm4, function (x) aa_props2[x])
645 PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues) 644 PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues)
646 PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AblActive,ArgActive,BtkActive,CskActive,FynActive,HckActive,JAk2Active,LckActive,LynActive,Pyk2Active,SrcActive,SykActive,YesActive) 645 PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AblActive,ArgActive,BtkActive,CskActive,FynActive,HckActive,JAk2Active,LckActive,LynActive,Pyk2Active,SrcActive,SykActive,YesActive)
647 RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$AllActive,decreasing = FALSE),] 646 RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$AllActive,decreasing = FALSE),]
648 # PepRankHead<-c(1:9,"Sequence","RPMS","PMS") 647 # PepRankHead<-c(1:9,"Sequence","RPMS","PMS")
649 # RanksPeptides<-rbind.data.frame(PepRankHead,PeptidesWithRanks) 648 # RanksPeptides<-rbind.data.frame(PepRankHead,PeptidesWithRanks)
650 head(RanksPeptides) 649 #head(RanksPeptides)
651 650
652 651
653 #now I have to score the negative sequences... for some reason 652 #now I have to score the negative sequences... for some reason
654 #write up how we transfect with lipofectamine 653 #write up how we transfect with lipofectamine
655 #3,4,5 questions 654 #3,4,5 questions
656 655
657 #PAUSED EHRE AT 4:50, HOPING THAT FIXING MINERVOTHING SO THAT LEFT SPACES WORKS FIXES A THING. OTHERWISE 656 #PAUSED EHRE AT 4:50, HOPING THAT FIXING MINERVOTHING SO THAT LEFT SPACES WORKS FIXES A THING. OTHERWISE
658 #I FUCKED WITH THE MCC TABLE AND NEED TO FINISH IT 657 #I FUCKED WITH THE MCC TABLE AND NEED TO FINISH IT
659 658
660 ThisKinBlanks<-rep(1,times=17) 659 ThisKinBlanks<-rep(1,times=17)
661 ThisKinTable<-rbind(ThisKinTable,ThisKinBlanks) 660 #indx <- sapply(breast, is.factor)
661 #ThisKinTable[indx] <- lapply(ThisKinTable[indx], function(x) as.character(x))
662 ThisKinTable$SetOfAAs<-as.character(ThisKinTable$SetOfAAs)
663
664 #ThisKinTest<-rbind.data.frame(ThisKinTable,ThisKinBlanks)
665 ThisKinTable<-rbind.data.frame(ThisKinTable,ThisKinBlanks)
662 666
663 NegativeScores<-rep(NA,times=nrow(NegativeSubstrateList)) 667 NegativeScores<-rep(NA,times=nrow(NegativeSubstrateList))
664 NegativeWeirdScores<-rep(NA,times=nrow(NegativeSubstrateList)) 668 NegativeWeirdScores<-rep(NA,times=nrow(NegativeSubstrateList))
665 for (v in 1:nrow(NegativeSubstrateList)) { 669 for (v in 1:nrow(NegativeSubstrateList)) {
666 motif<-NegativeSubstrateList[v,2] 670 motif<-NegativeSubstrateList[v,2]
772 # write.xlsx(NegativeWithScores,file = FILENAME, sheetName = "Negative Sequences Scored",col.names = TRUE,row.names = FALSE,append = TRUE) 776 # write.xlsx(NegativeWithScores,file = FILENAME, sheetName = "Negative Sequences Scored",col.names = TRUE,row.names = FALSE,append = TRUE)
773 # write.xlsx(Characterization,file = FILENAME,sheetName = "Characterization Table",col.names = TRUE,row.names = FALSE,append = TRUE) 777 # write.xlsx(Characterization,file = FILENAME,sheetName = "Characterization Table",col.names = TRUE,row.names = FALSE,append = TRUE)
774 # write.xlsx(RanksPeptides,file = FILENAME,sheetName = "Ranked Generated Peptides",col.names = FALSE,row.names = FALSE,append = TRUE) 778 # write.xlsx(RanksPeptides,file = FILENAME,sheetName = "Ranked Generated Peptides",col.names = FALSE,row.names = FALSE,append = TRUE)
775 # write.xlsx(positivewithscores,file = FILENAME, sheetName = "Positive Sequences Scored",col.names = FALSE,row.names = FALSE,append = TRUE) 779 # write.xlsx(positivewithscores,file = FILENAME, sheetName = "Positive Sequences Scored",col.names = FALSE,row.names = FALSE,append = TRUE)
776 write.table(x=c("Characterzation Table"),file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",") 780 write.table(x=c("Characterzation Table"),file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
777 write.table(Characterization,file = FILENAME2, col.names = TRUE,row.names = FALSE, append = TRUE,sep = ",") 781 header<-colnames(Characterization)
778 782 Characterization<-rbind.data.frame(header,Characterization)
779 783 write.table(Characterization,file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
780 write.table(RanksPeptides,file = FILENAME3,append = TRUE,row.names = FALSE,col.names = TRUE,sep = ",") 784
781 785 # header<-colnames(RanksPeptides)
782 786 # RanksPeptides<-rbind.data.frame(header,RanksPeptides)
787 write.table(RanksPeptides,file = FILENAME3,append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",")
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