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

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8:927eaf73feca

# require(rJava)
# require(xlsxjars)
# require(xlsx)
# # require(readxl)

View(SDtable)
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]))}

Positionp7<-which(goodones[,15] %in% TRUE)
if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}

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",
               "13"="P", "14"="Q", "15"="R", "16"="S", "17"="T", "18"="V", "19"="W", "20"="Y")
aa_props2<-c(1="A")

Positionm7<-sapply(Positionm7, function (x) aa_props2[x])
Positionm6<-sapply(Positionm6, function (x) aa_props2[x])
Positionm5<-sapply(Positionm5, function (x) aa_props2[x])
Positionm4<-sapply(Positionm4, function (x) aa_props2[x])

PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues)
PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AblActive,ArgActive,BtkActive,CskActive,FynActive,HckActive,JAk2Active,LckActive,LynActive,Pyk2Active,SrcActive,SykActive,YesActive)
RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$AllActive,decreasing = FALSE),]
# PepRankHead<-c(1:9,"Sequence","RPMS","PMS")
# RanksPeptides<-rbind.data.frame(PepRankHead,PeptidesWithRanks)
head(RanksPeptides)


#now I have to score the negative sequences... for some reason
#write up how we transfect with lipofectamine
#3,4,5 questions

#PAUSED EHRE AT 4:50, HOPING THAT FIXING MINERVOTHING SO THAT LEFT SPACES WORKS FIXES A THING.  OTHERWISE
#I FUCKED WITH THE MCC TABLE AND NEED TO FINISH IT 

ThisKinBlanks<-rep(1,times=17)
ThisKinTable<-rbind(ThisKinTable,ThisKinBlanks)

NegativeScores<-rep(NA,times=nrow(NegativeSubstrateList))
NegativeWeirdScores<-rep(NA,times=nrow(NegativeSubstrateList))
for (v in 1:nrow(NegativeSubstrateList)) {
  motif<-NegativeSubstrateList[v,2]

# write.xlsx(NegativeWithScores,file = FILENAME, sheetName = "Negative Sequences Scored",col.names = TRUE,row.names = FALSE,append = TRUE)
# write.xlsx(Characterization,file = FILENAME,sheetName = "Characterization Table",col.names = TRUE,row.names = FALSE,append = TRUE)
# write.xlsx(RanksPeptides,file = FILENAME,sheetName = "Ranked Generated Peptides",col.names = FALSE,row.names = FALSE,append = TRUE)
# write.xlsx(positivewithscores,file = FILENAME, sheetName = "Positive Sequences Scored",col.names = FALSE,row.names = FALSE,append = TRUE)
write.table(x=c("Characterzation Table"),file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
write.table(Characterization,file = FILENAME2, col.names = TRUE,row.names = FALSE, append = TRUE,sep = ",")


write.table(RanksPeptides,file = FILENAME3,append = TRUE,row.names = FALSE,col.names = TRUE,sep = ",")

9:f80306fc5d69

# require(rJava)
# require(xlsxjars)
# require(xlsx)
# # require(readxl)

#View(SDtable)
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]))}

Positionp7<-which(goodones[,15] %in% TRUE)
if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}

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",
               "13"="P", "14"="Q", "15"="R", "16"="S", "17"="T", "18"="V", "19"="W", "20"="Y")

Positionm7<-sapply(Positionm7, function (x) aa_props2[x])
Positionm6<-sapply(Positionm6, function (x) aa_props2[x])
Positionm5<-sapply(Positionm5, function (x) aa_props2[x])
Positionm4<-sapply(Positionm4, function (x) aa_props2[x])

PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues)
PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AblActive,ArgActive,BtkActive,CskActive,FynActive,HckActive,JAk2Active,LckActive,LynActive,Pyk2Active,SrcActive,SykActive,YesActive)
RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$AllActive,decreasing = FALSE),]
# PepRankHead<-c(1:9,"Sequence","RPMS","PMS")
# RanksPeptides<-rbind.data.frame(PepRankHead,PeptidesWithRanks)
#head(RanksPeptides)


#now I have to score the negative sequences... for some reason
#write up how we transfect with lipofectamine
#3,4,5 questions

#PAUSED EHRE AT 4:50, HOPING THAT FIXING MINERVOTHING SO THAT LEFT SPACES WORKS FIXES A THING.  OTHERWISE
#I FUCKED WITH THE MCC TABLE AND NEED TO FINISH IT 

ThisKinBlanks<-rep(1,times=17)
#indx <- sapply(breast, is.factor)
#ThisKinTable[indx] <- lapply(ThisKinTable[indx], function(x) as.character(x))
ThisKinTable$SetOfAAs<-as.character(ThisKinTable$SetOfAAs)

#ThisKinTest<-rbind.data.frame(ThisKinTable,ThisKinBlanks)
ThisKinTable<-rbind.data.frame(ThisKinTable,ThisKinBlanks)

NegativeScores<-rep(NA,times=nrow(NegativeSubstrateList))
NegativeWeirdScores<-rep(NA,times=nrow(NegativeSubstrateList))
for (v in 1:nrow(NegativeSubstrateList)) {
  motif<-NegativeSubstrateList[v,2]

# write.xlsx(NegativeWithScores,file = FILENAME, sheetName = "Negative Sequences Scored",col.names = TRUE,row.names = FALSE,append = TRUE)
# write.xlsx(Characterization,file = FILENAME,sheetName = "Characterization Table",col.names = TRUE,row.names = FALSE,append = TRUE)
# write.xlsx(RanksPeptides,file = FILENAME,sheetName = "Ranked Generated Peptides",col.names = FALSE,row.names = FALSE,append = TRUE)
# write.xlsx(positivewithscores,file = FILENAME, sheetName = "Positive Sequences Scored",col.names = FALSE,row.names = FALSE,append = TRUE)
write.table(x=c("Characterzation Table"),file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
header<-colnames(Characterization)
Characterization<-rbind.data.frame(header,Characterization)
write.table(Characterization,file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")

# header<-colnames(RanksPeptides)
# RanksPeptides<-rbind.data.frame(header,RanksPeptides)
write.table(RanksPeptides,file = FILENAME3,append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",")