Mercurial > repos > jfb > kinatest_r_7_7testing
view kinatestid_r/Kinatest-R_part2.R @ 13:d71eb1d66a88 draft
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| author | jfb |
|---|---|
| date | Thu, 08 Feb 2018 15:10:42 -0500 |
| parents | f80306fc5d69 |
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#test myself: this script should take in amino acids for each of the 9 positions and give out every single combination of those AAs #need to do following: fix it so that the accession numbers stay with the substrates, #also the neg false constant is totaly unphos'd Ys found by FASTA-2-CSV system# uniprot #HOW MANY: IF THERE'S two aas in each position you get 2^9, so I assume the numbers are: #(number in position-4)*(number in position -3)*(number in position -2)...=total # 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]))} 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]))} 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]) Positionm3<-sapply(Positionm3, function (x) aa_props2[x]) Positionm2<-sapply(Positionm2, function (x) aa_props2[x]) Positionm1<-sapply(Positionm1, function (x) aa_props2[x]) Positiond0<-sapply(Positiond0, function (x) aa_props2[x]) Positionp1<-sapply(Positionp1, function (x) aa_props2[x]) Positionp2<-sapply(Positionp2, function (x) aa_props2[x]) Positionp3<-sapply(Positionp3, function (x) aa_props2[x]) Positionp4<-sapply(Positionp4, function (x) aa_props2[x]) Positionp5<-sapply(Positionp5, function (x) aa_props2[x]) Positionp6<-sapply(Positionp6, function (x) aa_props2[x]) Positionp7<-sapply(Positionp7, function (x) aa_props2[x]) # Positionm7<-c("D","H","N","V") # Positionm6<-c("E","V") # Positionm5<-c("D","H") # Positionm4<-c("D","N") # Positionm3<-c("D","E","F","Q") # Positionm2<-c("D","N","Q","S") # Positionm1<-c("F","I","L") # Positiond0<-c("Y") # Positionp1<-c("A","E") # Positionp2<-c("T","S","Q","E") # Positionp3<-c("V") # Positionp4<-c("K") # Positionp5<-c("K") # Positionp6<-c("K") # Positionp7<-c("R") #this is where the amino acids for each position are given. m means minus, p mean plus ######################################## # ScreenerFilename<-"C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls" screaner<-read.csv(ScreenerFilename, header = FALSE, stringsAsFactors = FALSE) Abl<-screaner[2:25,] Arg<-screaner[27:50,] Btk<-screaner[52:75,] Csk<-screaner[77:100,] Fyn<-screaner[102:125,] Hck<-screaner[127:150,] JAK2<-screaner[152:175,] Lck<-screaner[177:200,] Lyn<-screaner[202:225,] Pyk2<-screaner[227:250,] Src<-screaner[252:275,] Syk<-screaner[277:300,] Yes<-screaner[302:325,] #two questions: why are we doing BTK when we already have a bioninformatics page about it? #two I reran everything and only get 96 positions of interest in the SD table #Do_You_want_An_Excel_Output_Questionmark<-"NO" GeneratedPeptidesFile<-"GeneratedPeptidesFile.csv" # Abl<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 4) # Arg<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 5) # Btk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 6) # Csk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 7) # Fyn<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 8) # Hck<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 9) # JAK2<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 10) # Lck<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 11) # Lyn<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 12) # Pyk2<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 13) # Src<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 14) # Syk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 15) # Yes<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 16) # "A"=1 "C"=2 "D"=3 "E"=4 "F"=5 "G"=6 "H"=7 "I"=8 "K"=9 "L"=10 "M"=11 "N"=12 "P"=13 "Q"=14 "R"=15 "S"=16 "T"=17 "V"=18 "W"=19 "Y"=20 aa_props <- c("A"=A, "C"=C, "D"=D, "E"=E, "F"=F,"G"=G,"H"=H,"I"=I,"K"=K,"L"=L,"M"=M,"N"=N,"P"=P,"Q"=Q,"R"=R, "S"=S,"T"=T,"V"=V,"W"=W,"Y"=Y,"xY"=Y,"O"=21) number15<-sapply(Positionm7, function (x) aa_props[x]) number14<-sapply(Positionm6, function (x) aa_props[x]) number13<-sapply(Positionm5, function (x) aa_props[x]) number1 <- sapply(Positionm4, function (x) aa_props[x]) number2 <- sapply(Positionm3, function (x) aa_props[x]) number3 <- sapply(Positionm2, function (x) aa_props[x]) number4 <- sapply(Positionm1, function (x) aa_props[x]) number5 <- sapply(Positiond0, function (x) aa_props[x]) number6 <- sapply(Positionp1, function (x) aa_props[x]) number7 <- sapply(Positionp2, function (x) aa_props[x]) number8 <- sapply(Positionp3, function (x) aa_props[x]) number9 <- sapply(Positionp4, function (x) aa_props[x]) number10<-sapply(Positionp5, function (x) aa_props[x]) number11<-sapply(Positionp6, function (x) aa_props[x]) number12<-sapply(Positionp7, function (x) aa_props[x]) # number1<-Positionm4 # number2<-Positionm3 # number3<-Positionm2 # number4<-Positionm1 # number5<-Positiond0 # number6<-Positionp1 # number7<-Positionp2 # number8<-Positionp3 # number9<-Positionp4 ############################# #here I create the Abl seqs with proper value for each number if (1==0){ Ablnumber1<- gsub("A",A,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("C",C,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("D",D,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("E",E,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("F",F,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("G",G,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("H",H,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("I",I,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("K",K,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("L",L,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("M",M,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("N",N,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("P",P,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("Q",Q,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("R",R,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("S",S,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("T",T,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("V",V,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("W",W,Ablnumber1,perl = TRUE) Ablnumber1<- gsub("Y",Y,Ablnumber1,perl = TRUE) Ablnumber2<- gsub("A",A,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("C",C,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("D",D,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("E",E,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("F",F,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("G",G,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("H",H,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("I",I,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("K",K,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("L",L,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("M",M,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("N",N,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("P",P,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("Q",Q,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("R",R,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("S",S,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("T",T,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("V",V,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("W",W,Ablnumber2,perl = TRUE) Ablnumber2<- gsub("Y",Y,Ablnumber2,perl = TRUE) Ablnumber3<- gsub("A",A,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("C",C,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("D",D,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("E",E,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("F",F,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("G",G,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("H",H,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("I",I,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("K",K,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("L",L,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("M",M,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("N",N,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("P",P,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("Q",Q,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("R",R,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("S",S,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("T",T,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("V",V,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("W",W,Ablnumber3,perl = TRUE) Ablnumber3<- gsub("Y",Y,Ablnumber3,perl = TRUE) Ablnumber4<- gsub("A",A,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("C",C,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("D",D,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("E",E,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("F",F,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("G",G,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("H",H,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("I",I,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("K",K,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("L",L,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("M",M,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("N",N,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("P",P,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("Q",Q,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("R",R,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("S",S,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("T",T,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("V",V,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("W",W,Ablnumber4,perl = TRUE) Ablnumber4<- gsub("Y",Y,Ablnumber4,perl = TRUE) Ablnumber5<- gsub("A",A,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("C",C,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("D",D,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("E",E,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("F",F,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("G",G,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("H",H,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("I",I,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("K",K,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("L",L,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("M",M,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("N",N,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("P",P,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("Q",Q,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("R",R,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("S",S,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("T",T,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("V",V,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("W",W,Ablnumber5,perl = TRUE) Ablnumber5<- gsub("Y",Y,Ablnumber5,perl = TRUE) Ablnumber6<- gsub("A",A,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("C",C,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("D",D,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("E",E,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("F",F,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("G",G,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("H",H,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("I",I,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("K",K,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("L",L,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("M",M,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("N",N,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("P",P,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("Q",Q,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("R",R,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("S",S,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("T",T,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("V",V,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("W",W,Ablnumber6,perl = TRUE) Ablnumber6<- gsub("Y",Y,Ablnumber6,perl = TRUE) Ablnumber7<- gsub("A",A,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("C",C,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("D",D,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("E",E,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("F",F,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("G",G,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("H",H,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("I",I,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("K",K,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("L",L,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("M",M,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("N",N,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("P",P,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("Q",Q,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("R",R,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("S",S,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("T",T,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("V",V,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("W",W,Ablnumber7,perl = TRUE) Ablnumber7<- gsub("Y",Y,Ablnumber7,perl = TRUE) Ablnumber8<- gsub("A",A,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("C",C,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("D",D,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("E",E,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("F",F,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("G",G,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("H",H,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("I",I,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("K",K,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("L",L,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("M",M,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("N",N,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("P",P,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("Q",Q,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("R",R,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("S",S,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("T",T,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("V",V,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("W",W,Ablnumber8,perl = TRUE) Ablnumber8<- gsub("Y",Y,Ablnumber8,perl = TRUE) Ablnumber9<- gsub("A",A,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("C",C,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("D",D,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("E",E,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("F",F,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("G",G,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("H",H,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("I",I,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("K",K,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("L",L,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("M",M,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("N",N,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("P",P,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("Q",Q,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("R",R,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("S",S,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("T",T,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("V",V,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("W",W,Ablnumber9,perl = TRUE) Ablnumber9<- gsub("Y",Y,Ablnumber9,perl = TRUE) } ######################################## total=length(Positionp7)*length(Positionp6)*length(Positionp5)*length(Positionp4)*length(Positionp3)*(length(Positionp2))*length(Positionp1)* length(Positiond0)*length(Positionm1)*length(Positionm2)*length(Positionm3)*length(Positionm4)*length(Positionm5)*length(Positionm6)*length(Positionm7) #this is just a way to doublecheck that the length of the generated peptides vector is correct GeneratedPeptides<-rep(NA, times=total*15) GeneratedPeptides<-matrix(data = GeneratedPeptides,ncol = 15) NumeratedPeptides<-GeneratedPeptides #create an empty vector of correct length by finding the number of each AAs per position and multiplying them count<-0 for (t in 1:length(Positionm7)) { for (s in 1:length(Positionm6)) { for (r in 1:length(Positionm5)) { for (i in 1:length(Positionm4)) { for (j in 1:length(Positionm3)) { for (k in 1:length(Positionm2)) { for (l in 1:length(Positionm1)) { for (m in 1:length(Positiond0)) { for (n in 1:length(Positionp1)) { for (o in 1:length(Positionp2)) { for (p in 1:length(Positionp3)) { for (q in 1:length(Positionp4)) { for (u in 1:length(Positionp5)) { for (v in 1:length(Positionp6)) { for (w in 1:length(Positionp7)) { # i=1 # j=1 # k=1 # l=1 # m=1 # n=1 # o=1 # p=1 # q=1 # #for every single position, increment the count number, create a peptide using the AAs at that position #then put them together into the generated peptides sequencex count<-count+1 tabulation<-c(Positionm7[t],Positionm6[s],Positionm5[r],Positionm4[i],Positionm3[j],Positionm2[k],Positionm1[l],Positiond0[m],Positionp1[n], Positionp2[o],Positionp3[p],Positionp4[q],Positionp5[u],Positionp6[v],Positionp7[w]) numeration<-c(number15[t],number14[s],number13[r],number1[i],number2[j],number3[k],number4[l],number5[m],number6[n],number7[o],number8[p],number9[q],number10[u],number11[v], number12[w]) #tabulation<-paste(tabulation, sep="", collapse="") GeneratedPeptides[count,1:15]<-tabulation NumeratedPeptides[count,1:15]<-numeration } } } } } } } } } } } } } } } #################################################################### #now here I use the Endogenous Probabilty matrix from the previous script, which is called EMPtable #to score the created peptides ThisKinTable<-EPMtableu#[1:nrow(SDtable),] TKTcolumn<-c(data=rep(1,times=21)) TKTcolumn<-as.matrix(TKTcolumn,ncol=1) ThisKinTable<-cbind(TKTcolumn,ThisKinTable) ThisKinGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) ThisKinGenWeirdScore<-rep(NA,times=nrow(GeneratedPeptides)) for (x in 1:nrow(GeneratedPeptides)){ Scoringpeptide<-NumeratedPeptides[x,1:15] Scoringpeptide<-Scoringpeptide+1 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]* ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]* #ThisKinTable[as.numeric(Scoringpeptide[8]),10]* ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]* ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17] ThisKinGeneratedScores[x]<-ThisKinTableScore ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2]))) ThisKinGenWeirdScore[x]<-ThisKinTableScore } AblGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) ArgGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) BtkGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) CskGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) FynGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) HckGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) JAK2GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) LckGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) LynGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) Pyk2GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) SrcGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) SykGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) YesGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides)) for (x in 1:nrow(GeneratedPeptides)){ Scoringpeptide<-NumeratedPeptides[x,1:15] AblScore<-Abl[Scoringpeptide[1],2]*Abl[Scoringpeptide[2],3]*Abl[Scoringpeptide[3],4]*Abl[Scoringpeptide[4],5]*Abl[Scoringpeptide[5],6]*Abl[Scoringpeptide[6],7]* Abl[Scoringpeptide[7],8]*Abl[Scoringpeptide[9],10]*Abl[Scoringpeptide[10],11]*Abl[Scoringpeptide[11],12]*Abl[Scoringpeptide[12],13]* Abl[Scoringpeptide[13],14]*Abl[Scoringpeptide[14],15]*Abl[Scoringpeptide[15],16] AblGeneratedScores[x]<-AblScore ArgScore<-Arg[Scoringpeptide[1],2]*Arg[Scoringpeptide[2],3]*Arg[Scoringpeptide[3],4]*Arg[Scoringpeptide[4],5]*Arg[Scoringpeptide[5],6]*Arg[Scoringpeptide[6],7]* Arg[Scoringpeptide[7],8]*Arg[Scoringpeptide[9],10]*Arg[Scoringpeptide[10],11]*Arg[Scoringpeptide[11],12]*Arg[Scoringpeptide[12],13]* Arg[Scoringpeptide[13],14]*Arg[Scoringpeptide[14],15]*Arg[Scoringpeptide[15],16] ArgGeneratedScores[x]<-ArgScore BtkScore<-Btk[Scoringpeptide[1],2]*Btk[Scoringpeptide[2],3]*Btk[Scoringpeptide[3],4]*Btk[Scoringpeptide[4],5]*Btk[Scoringpeptide[5],6]*Btk[Scoringpeptide[6],7]* Btk[Scoringpeptide[7],8]*Btk[Scoringpeptide[9],10]*Btk[Scoringpeptide[10],11]*Btk[Scoringpeptide[11],12]*Btk[Scoringpeptide[12],13]* Btk[Scoringpeptide[13],14]*Btk[Scoringpeptide[14],15]*Btk[Scoringpeptide[15],16] BtkGeneratedScores[x]<-BtkScore CskScore<-Csk[Scoringpeptide[1],2]*Csk[Scoringpeptide[2],3]*Csk[Scoringpeptide[3],4]*Csk[Scoringpeptide[4],5]*Csk[Scoringpeptide[5],6]*Csk[Scoringpeptide[6],7]* Csk[Scoringpeptide[7],8]*Csk[Scoringpeptide[9],10]*Csk[Scoringpeptide[10],11]*Csk[Scoringpeptide[11],12]*Csk[Scoringpeptide[12],13]* Csk[Scoringpeptide[13],14]*Csk[Scoringpeptide[14],15]*Csk[Scoringpeptide[15],16] CskGeneratedScores[x]<-CskScore FynScore<-Fyn[Scoringpeptide[1],2]*Fyn[Scoringpeptide[2],3]*Fyn[Scoringpeptide[3],4]*Fyn[Scoringpeptide[4],5]*Fyn[Scoringpeptide[5],6]*Fyn[Scoringpeptide[6],7]* Fyn[Scoringpeptide[7],8]*Fyn[Scoringpeptide[9],10]*Fyn[Scoringpeptide[10],11]*Fyn[Scoringpeptide[11],12]*Fyn[Scoringpeptide[12],13]* Fyn[Scoringpeptide[13],14]*Fyn[Scoringpeptide[14],15]*Fyn[Scoringpeptide[15],16] FynGeneratedScores[x]<-FynScore HckScore<-Hck[Scoringpeptide[1],2]*Hck[Scoringpeptide[2],3]*Hck[Scoringpeptide[3],4]*Hck[Scoringpeptide[4],5]*Hck[Scoringpeptide[5],6]*Hck[Scoringpeptide[6],7]* Hck[Scoringpeptide[7],8]*Hck[Scoringpeptide[9],10]*Hck[Scoringpeptide[10],11]*Hck[Scoringpeptide[11],12]*Hck[Scoringpeptide[12],13]* Hck[Scoringpeptide[13],14]*Hck[Scoringpeptide[14],15]*Hck[Scoringpeptide[15],16] HckGeneratedScores[x]<-HckScore JAK2Score<-JAK2[Scoringpeptide[1],2]*JAK2[Scoringpeptide[2],3]*JAK2[Scoringpeptide[3],4]*JAK2[Scoringpeptide[4],5]*JAK2[Scoringpeptide[5],6]*JAK2[Scoringpeptide[6],7]* JAK2[Scoringpeptide[7],8]*JAK2[Scoringpeptide[9],10]*JAK2[Scoringpeptide[10],11]*JAK2[Scoringpeptide[11],12]*JAK2[Scoringpeptide[12],13]* JAK2[Scoringpeptide[13],14]*JAK2[Scoringpeptide[14],15]*JAK2[Scoringpeptide[15],16] JAK2GeneratedScores[x]<-JAK2Score LckScore<-Lck[Scoringpeptide[1],2]*Lck[Scoringpeptide[2],3]*Lck[Scoringpeptide[3],4]*Lck[Scoringpeptide[4],5]*Lck[Scoringpeptide[5],6]*Lck[Scoringpeptide[6],7]* Lck[Scoringpeptide[7],8]*Lck[Scoringpeptide[9],10]*Lck[Scoringpeptide[10],11]*Lck[Scoringpeptide[11],12]*Lck[Scoringpeptide[12],13]* Lck[Scoringpeptide[13],14]*Lck[Scoringpeptide[14],15]*Lck[Scoringpeptide[15],16] LckGeneratedScores[x]<-LckScore LynScore<-Lyn[Scoringpeptide[1],2]*Lyn[Scoringpeptide[2],3]*Lyn[Scoringpeptide[3],4]*Lyn[Scoringpeptide[4],5]*Lyn[Scoringpeptide[5],6]*Lyn[Scoringpeptide[6],7]* Lyn[Scoringpeptide[7],8]*Lyn[Scoringpeptide[9],10]*Lyn[Scoringpeptide[10],11]*Lyn[Scoringpeptide[11],12]*Lyn[Scoringpeptide[12],13]* Lyn[Scoringpeptide[13],14]*Lyn[Scoringpeptide[14],15]*Lyn[Scoringpeptide[15],16] LynGeneratedScores[x]<-LynScore Pyk2Score<-Pyk2[Scoringpeptide[1],2]*Pyk2[Scoringpeptide[2],3]*Pyk2[Scoringpeptide[3],4]*Pyk2[Scoringpeptide[4],5]*Pyk2[Scoringpeptide[5],6]*Pyk2[Scoringpeptide[6],7]* Pyk2[Scoringpeptide[7],8]*Pyk2[Scoringpeptide[9],10]*Pyk2[Scoringpeptide[10],11]*Pyk2[Scoringpeptide[11],12]*Pyk2[Scoringpeptide[12],13]* Pyk2[Scoringpeptide[13],14]*Pyk2[Scoringpeptide[14],15]*Pyk2[Scoringpeptide[15],16] Pyk2GeneratedScores[x]<-Pyk2Score SrcScore<-Src[Scoringpeptide[1],2]*Src[Scoringpeptide[2],3]*Src[Scoringpeptide[3],4]*Src[Scoringpeptide[4],5]*Src[Scoringpeptide[5],6]*Src[Scoringpeptide[6],7]* Src[Scoringpeptide[7],8]*Src[Scoringpeptide[9],10]*Src[Scoringpeptide[10],11]*Src[Scoringpeptide[11],12]*Src[Scoringpeptide[12],13]* Src[Scoringpeptide[13],14]*Src[Scoringpeptide[14],15]*Src[Scoringpeptide[15],16] SrcGeneratedScores[x]<-SrcScore SykScore<-Syk[Scoringpeptide[1],2]*Syk[Scoringpeptide[2],3]*Syk[Scoringpeptide[3],4]*Syk[Scoringpeptide[4],5]*Syk[Scoringpeptide[5],6]*Syk[Scoringpeptide[6],7]* Syk[Scoringpeptide[7],8]*Syk[Scoringpeptide[9],10]*Syk[Scoringpeptide[10],11]*Syk[Scoringpeptide[11],12]*Syk[Scoringpeptide[12],13]* Syk[Scoringpeptide[13],14]*Syk[Scoringpeptide[14],15]*Syk[Scoringpeptide[15],16] SykGeneratedScores[x]<-SykScore YesScore<-Yes[Scoringpeptide[1],2]*Yes[Scoringpeptide[2],3]*Yes[Scoringpeptide[3],4]*Yes[Scoringpeptide[4],5]*Yes[Scoringpeptide[5],6]*Yes[Scoringpeptide[6],7]* Yes[Scoringpeptide[7],8]*Yes[Scoringpeptide[9],10]*Yes[Scoringpeptide[10],11]*Yes[Scoringpeptide[11],12]*Yes[Scoringpeptide[12],13]* Yes[Scoringpeptide[13],14]*Yes[Scoringpeptide[14],15]*Yes[Scoringpeptide[15],16] YesGeneratedScores[x]<-YesScore # ThisKinTableScore<-ThisKinTable[as.numeric(Scoringpeptide[1]),3]*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]* # ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]* # ThisKinTable[as.numeric(Scoringpeptide[7]),9]*ThisKinTable[as.numeric(Scoringpeptide[8]),10]*ThisKinTable[as.numeric(Scoringpeptide[9]),11] # ThisKinGeneratedScores[x]<-ThisKinTableScore } AblNorm<-1/as.numeric(Abl[22,1]) AblThresh<-as.numeric(Abl[24,1]) AblTrueThresh<-((AblThresh*AblNorm)/(100-AblThresh)) AblActive<-unlist(AblGeneratedScores)>AblTrueThresh ArgNorm<-1/as.numeric(Arg[22,1]) ArgThresh<-as.numeric(Arg[24,1]) ArgTrueThresh<-((ArgThresh*ArgNorm)/(100-ArgThresh)) ArgActive<-unlist(ArgGeneratedScores)>ArgTrueThresh BtkNorm<-1/as.numeric(Btk[22,1]) BtkThresh<-as.numeric(Btk[24,1]) BtkTrueThresh<-((BtkThresh*BtkNorm)/(100-BtkThresh)) BtkActive<-unlist(BtkGeneratedScores)>BtkTrueThresh CskNorm<-1/as.numeric(Csk[22,1]) CskThresh<-as.numeric(Csk[24,1]) CskTrueThresh<-((CskThresh*CskNorm)/(100-CskThresh)) CskActive<-(CskGeneratedScores)>CskTrueThresh FynNorm<-1/as.numeric(Fyn[22,1]) FynThresh<-as.numeric(Fyn[24,1]) FynTrueThresh<-((FynThresh*FynNorm)/(100-FynThresh)) FynActive<-unlist(FynGeneratedScores)>FynTrueThresh HckNorm<-1/as.numeric(Hck[22,1]) HckThresh<-as.numeric(Hck[24,1]) HckTrueThresh<-((HckThresh*HckNorm)/(100-HckThresh)) HckActive<-unlist(HckGeneratedScores)>HckTrueThresh JAK2Norm<-1/as.numeric(JAK2[22,1]) JAK2Thresh<-as.numeric(JAK2[24,1]) JAK2TrueThresh<-((JAK2Thresh*JAK2Norm)/(100-JAK2Thresh)) JAk2Active<-unlist(JAK2GeneratedScores)>JAK2TrueThresh LckNorm<-1/as.numeric(Lck[22,1]) LckThresh<-as.numeric(Lck[24,1]) LckTrueThresh<-((LckThresh*LckNorm)/(100-LckThresh)) LckActive<-unlist(LckGeneratedScores)>LckTrueThresh LynNorm<-1/as.numeric(Lyn[22,1]) LynThresh<-as.numeric(Lyn[24,1]) LynTrueThresh<-((LynThresh*LynNorm)/(100-LynThresh)) LynActive<-unlist(LynGeneratedScores)>LynTrueThresh Pyk2Norm<-1/as.numeric(Pyk2[22,1]) Pyk2Thresh<-as.numeric(Pyk2[24,1]) Pyk2TrueThresh<-((Pyk2Thresh*Pyk2Norm)/(100-Pyk2Thresh)) Pyk2Active<-unlist(Pyk2GeneratedScores)>Pyk2TrueThresh SrcNorm<-1/as.numeric(Src[22,1]) SrcThresh<-as.numeric(Src[24,1]) SrcTrueThresh<-((SrcThresh*SrcNorm)/(100-SrcThresh)) SrcActive<-unlist(SrcGeneratedScores)>SrcTrueThresh SykNorm<-1/as.numeric(Syk[22,1]) SykThresh<-as.numeric(Syk[24,1]) SykTrueThresh<-((SykThresh*SykNorm)/(100-SykThresh)) SykActive<-unlist(SykGeneratedScores)>SykTrueThresh YesNorm<-1/as.numeric(Yes[22,1]) YesThresh<-as.numeric(Yes[24,1]) YesTrueThresh<-((YesThresh*YesNorm)/(100-YesThresh)) YesActive<-unlist(YesGeneratedScores)>YesTrueThresh AllActive<-AblActive+ArgActive+BtkActive+CskActive+FynActive+HckActive+JAk2Active+LckActive+LynActive+Pyk2Active+SrcActive+SykActive+YesActive #Btkactive+ Scores<-ThisKinGeneratedScores ThresholdValues<-ThisKinGenWeirdScore FullMotifs<-rep("Z",times=nrow(GeneratedPeptides)) for (i in 1:nrow(GeneratedPeptides)) { motif<-GeneratedPeptides[i,1:15] motif<-paste(motif,sep = "", collapse = "") FullMotifs[i]<-motif } 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] motif<-unlist(strsplit(motif,"")) #if (length(motif)<9){print(v)}} # motif[1] <- sapply(motif[1], function (x) aa_props[x]) # motif[2] <- sapply(motif[2], function (x) aa_props[x]) # motif[3] <- sapply(motif[3], function (x) aa_props[x]) # motif[4] <- sapply(motif[4], function (x) aa_props[x]) # motif[5] <- sapply(motif[5], function (x) aa_props[x]) # motif[6] <- sapply(motif[6], function (x) aa_props[x]) # motif[7] <- sapply(motif[7], function (x) aa_props[x]) # motif[8] <- sapply(motif[8], function (x) aa_props[x]) # motif[9] <- sapply(motif[9], function (x) aa_props[x]) motif<- gsub(" ","O",motif) motif <- sapply(motif, function (x) aa_props[x]) Scoringpeptide<-motif Scoringpeptide<-Scoringpeptide+1 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]* ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]* #ThisKinTable[as.numeric(Scoringpeptide[8]),10]* ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]* ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17] NegativeScores[v]<-ThisKinTableScore ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2]))) NegativeWeirdScores[v]<-ThisKinTableScore*100 } negativesubstrates<-NegativeSubstrateList[,2] NegativeWithScores<-cbind(negativesubstrates,as.character(NegativeScores),as.character(NegativeWeirdScores)) #NEED TO HAVE THE NEGATIVE SUBSTRATES BE OUTPUTTED PositiveScores<-rep(NA,times=nrow(ImportedSubstrateList)) PositiveWeirdScores<-rep(NA,times=nrow(ImportedSubstrateList)) for (v in 1:nrow(ImportedSubstrateList)) { motif<-ImportedSubstrateList[v,4:18] motif<-unlist(motif) motif<- gsub("^$","O",motif) motif <- sapply(motif, function (x) aa_props[x]) Scoringpeptide<-motif Scoringpeptide<-Scoringpeptide+1 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]* ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]* #ThisKinTable[as.numeric(Scoringpeptide[8]),10]* ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]* ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17] PositiveScores[v]<-ThisKinTableScore ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2]))) PositiveWeirdScores[v]<-ThisKinTableScore*100 } positivesubstrates<-ImportedSubstrateList[,4:18] positivewithscores<-cbind.data.frame(positivesubstrates,PositiveScores,PositiveWeirdScores) #write down the transient transfection SOP and what we will be doing with them #write down the vector names I will be using #write down something about transforming bacteria and with what #90% whatevernness # TPninetyone<-length(PositiveWeirdScores[PositiveWeirdScores>=0.91]) # Senseninetyone<-TPninetyone/nrow(positivesubstrates) # # TNninetyone<-length(NegativeWeirdScores[NegativeWeirdScores<91]) # Specninetyone<-TNninetyone/100 #create the MCC table threshold<-c(1:100) threshold<-order(threshold,decreasing = TRUE) Truepositives<-c(1:100) Falsenegatives<-c(1:100) Sensitivity<-c(1:100) TrueNegatives<-c(1:100) FalsePositives<-c(1:100) Specificity<-c(1:100) Accuracy<-c(1:100) MCC<-c(1:100) EER<-c(1:100) #MAKE DAMN SURE THAT THE ACCESSION NUMBERS FOLLOW THE MOTIFS for (z in 1:100) { thres<-101-z Truepositives[z]<-length(PositiveWeirdScores[PositiveWeirdScores>=(thres)]) Falsenegatives[z]<-nrow(positivesubstrates)-Truepositives[z] Sensitivity[z]<-Truepositives[z]/(Falsenegatives[z]+Truepositives[z]) TrueNegatives[z]<-length(NegativeWeirdScores[NegativeWeirdScores<(thres)]) # at thresh 100 this should be 0, because it is total minus true negatives FalsePositives[z]<-nrow(NegativeSubstrateList)-TrueNegatives[z] Specificity[z]<-1-(TrueNegatives[z]/(FalsePositives[z]+TrueNegatives[z])) Accuracy[z]<-100*(Truepositives[z]+TrueNegatives[z])/(Falsenegatives[z]+FalsePositives[z]+TrueNegatives[z]+Truepositives[z]) MCC[z]<-((Truepositives[z]+TrueNegatives[z])-(Falsenegatives[z]+FalsePositives[z]))/sqrt(round(round(Truepositives[z]+Falsenegatives[z])*round(TrueNegatives[z]+FalsePositives[z])*round(Truepositives[z]+FalsePositives[z])*round(TrueNegatives[z]+Falsenegatives[z]))) EER[z]<-.01*(((1-(Sensitivity[z]))*(Truepositives[z]+Falsenegatives[z]))+(Specificity[z]*(1-(Truepositives[z]+Falsenegatives[z])))) } Characterization<-cbind.data.frame(threshold,Truepositives,Falsenegatives,Sensitivity,TrueNegatives,FalsePositives,Specificity,Accuracy,MCC,EER) positiveheader<-c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,"RPMS","PMS") positivewithscores<-rbind.data.frame(positiveheader,positivewithscores) negativeheader<-c("Substrate","RPMS","PMS") colnames(NegativeWithScores)<-negativeheader # 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 = ",")