Mercurial > repos > jfb > kinatest_r_7_7testing
view kinatestid_r/Kinatest-R_part1.R @ 13:d71eb1d66a88 draft
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| author | jfb |
|---|---|
| date | Thu, 08 Feb 2018 15:10:42 -0500 |
| parents | cf93d3535a31 |
| children |
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ImportedSubstrateList<- read.csv("input1", stringsAsFactors=FALSE) NegativeSubstrateList<- read.csv("input2", stringsAsFactors=FALSE) SubstrateBackgroundFrequency<- read.csv("input3", stringsAsFactors=FALSE) ScreenerFilename<-"screener" FILENAME<-"output1" FILENAME2<-"output2" FILENAME3<-"output3" OutputMatrix<-"KinaseMatrix.csv" CharacterizationTable<-"CharacterizationTableForThisKinase.csv" SDtable<-"SDtableforthisKinase" SiteSelectivityTable<-"SiteSelectivityForThisKinase" substrates<-matrix(rep("A",times=((nrow(ImportedSubstrateList)-1)*15)),ncol = 15) #SeqsToBeScored<-"asdasd" for (i in 2:nrow(ImportedSubstrateList)) { substratemotif<-ImportedSubstrateList[i,4:18] substratemotif[8]<-"Y" #substratemotif<-paste(substratemotif,sep = "",collapse = "") j=i-1 substratemotif<-unlist(substratemotif) substrates[j,1:15]<-substratemotif } # SpacesToOs<-c(""="O",) # substrates<-SpacesToOs[substrates] SubstrateBackgroundFrequency[nrow(SubstrateBackgroundFrequency),2] if(2==2){ Amean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),2]), na.rm=TRUE) Cmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),3]), na.rm=TRUE) Dmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),4]), na.rm=TRUE) Emean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),5]), na.rm=TRUE) Fmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),6]), na.rm=TRUE) Gmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),7]), na.rm=TRUE) Hmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),8]), na.rm=TRUE) Imean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),9]), na.rm=TRUE) Kmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),10]), na.rm=TRUE) Lmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),11]), na.rm=TRUE) Mmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),12]), na.rm=TRUE) Nmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),13]), na.rm=TRUE) Pmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),14]), na.rm=TRUE) Qmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),15]), na.rm=TRUE) Rmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),16]), na.rm=TRUE) Smean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),17]), na.rm=TRUE) Tmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),18]), na.rm=TRUE) Vmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),19]), na.rm=TRUE) Wmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),20]), na.rm=TRUE) Ymean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),21]), na.rm=TRUE) AllMeans<-c(Amean,Cmean,Dmean,Emean,Fmean,Gmean,Hmean,Imean,Kmean,Lmean,Mmean,Nmean,Pmean,Qmean,Rmean,Smean,Tmean,Vmean,Wmean,Ymean) Asd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),2]), na.rm=TRUE) Csd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),3]), na.rm=TRUE) Dsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),4]), na.rm=TRUE) Esd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),5]), na.rm=TRUE) Fsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),6]), na.rm=TRUE) Gsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),7]), na.rm=TRUE) Hsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),8]), na.rm=TRUE) Isd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),9]), na.rm=TRUE) Ksd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),10]), na.rm=TRUE) Lsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),11]), na.rm=TRUE) Msd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),12]), na.rm=TRUE) Nsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),13]), na.rm=TRUE) Psd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),14]), na.rm=TRUE) Qsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),15]), na.rm=TRUE) Rsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),16]), na.rm=TRUE) Ssd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),17]), na.rm=TRUE) Tsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),18]), na.rm=TRUE) Vsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),19]), na.rm=TRUE) Wsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),20]), na.rm=TRUE) Ysd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),21]), na.rm=TRUE) } AllSDs<-c(Asd,Csd,Dsd,Esd,Fsd,Gsd,Hsd,Isd,Ksd,Lsd,Msd,Nsd,Psd,Qsd,Rsd,Ssd,Tsd,Vsd,Wsd,Ysd) #this is subbackfreq SDs SBF_statisticalvalues<-cbind(AllMeans,AllSDs) #create the percent table if (1==1){ Column1<-substrates[,1] Column2<-substrates[,2] Column3<-substrates[,3] Column4<-substrates[,4] Column5<-substrates[,5] Column6<-substrates[,6] Column7<-substrates[,7] Column8<-substrates[,8] Column9<-substrates[,9] Column10<-substrates[,10] Column11<-substrates[,11] Column12<-substrates[,12] Column13<-substrates[,13] Column14<-substrates[,14] Column15<-substrates[,15] spaces1<-sum((Column1%in% "")) spaces2<-sum(Column2%in% "") spaces3<-sum(Column3%in% "") spaces4<-sum(Column4%in% "") spaces5<-sum(Column5%in% "") spaces6<-sum(Column6%in% "") spaces7<-sum(Column7%in% "") spaces8<-sum(Column8%in% "") spaces9<-sum(Column9%in% "") spaces10<-sum(Column10%in% "") spaces11<-sum(Column11%in% "") spaces12<-sum(Column12%in% "") spaces13<-sum(Column13%in% "") spaces14<-sum(Column14%in% "") spaces15<-sum(Column15%in% "") A1<-sum(Column1 %in% "A")/(length(Column1)-spaces1) A2<-sum(Column2 %in% "A")/(length(Column2)-spaces2) A3<-sum(Column3 %in% "A")/(length(Column3)-spaces3) A4<-sum(Column4 %in% "A")/(length(Column4)-spaces4) A5<-sum(Column5 %in% "A")/(length(Column5)-spaces5) A6<-sum(Column6 %in% "A")/(length(Column6)-spaces6) A7<-sum(Column7 %in% "A")/(length(Column7)-spaces7) A8<-sum(Column8 %in% "A")/(length(Column8)-spaces8) A9<-sum(Column9 %in% "A")/(length(Column9)-spaces9) A10<-sum(Column10 %in% "A")/(length(Column10)-spaces10) A11<-sum(Column11 %in% "A")/(length(Column11)-spaces11) A12<-sum(Column12 %in% "A")/(length(Column12)-spaces12) A13<-sum(Column13 %in% "A")/(length(Column13)-spaces13) A14<-sum(Column14 %in% "A")/(length(Column14)-spaces14) A15<-sum(Column15 %in% "A")/(length(Column15)-spaces15) AllAs<-cbind(A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,A13,A14,A15) C1<-sum(Column1 %in% "C")/(length(Column1)-spaces1) C2<-sum(Column2 %in% "C")/(length(Column2)-spaces2) C3<-sum(Column3 %in% "C")/(length(Column3)-spaces3) C4<-sum(Column4 %in% "C")/(length(Column4)-spaces4) C5<-sum(Column5 %in% "C")/(length(Column5)-spaces5) C6<-sum(Column6 %in% "C")/(length(Column6)-spaces6) C7<-sum(Column7 %in% "C")/(length(Column7)-spaces7) C8<-sum(Column8 %in% "C")/(length(Column8)-spaces8) C9<-sum(Column9 %in% "C")/(length(Column9)-spaces9) C10<-sum(Column10 %in% "C")/(length(Column10)-spaces10) C11<-sum(Column11 %in% "C")/(length(Column11)-spaces11) C12<-sum(Column12 %in% "C")/(length(Column12)-spaces12) C13<-sum(Column13 %in% "C")/(length(Column13)-spaces13) C14<-sum(Column14 %in% "C")/(length(Column14)-spaces14) C15<-sum(Column15 %in% "C")/(length(Column15)-spaces15) CllCs<-cbind(C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,C13,C14,C15) D1<-sum(Column1 %in% "D")/(length(Column1)-spaces1) D2<-sum(Column2 %in% "D")/(length(Column2)-spaces2) D3<-sum(Column3 %in% "D")/(length(Column3)-spaces3) D4<-sum(Column4 %in% "D")/(length(Column4)-spaces4) D5<-sum(Column5 %in% "D")/(length(Column5)-spaces5) D6<-sum(Column6 %in% "D")/(length(Column6)-spaces6) D7<-sum(Column7 %in% "D")/(length(Column7)-spaces7) D8<-sum(Column8 %in% "D")/(length(Column8)-spaces8) D9<-sum(Column9 %in% "D")/(length(Column9)-spaces9) D10<-sum(Column10 %in% "D")/(length(Column10)-spaces10) D11<-sum(Column11 %in% "D")/(length(Column11)-spaces11) D12<-sum(Column12 %in% "D")/(length(Column12)-spaces12) D13<-sum(Column13 %in% "D")/(length(Column13)-spaces13) D14<-sum(Column14 %in% "D")/(length(Column14)-spaces14) D15<-sum(Column15 %in% "D")/(length(Column15)-spaces15) DllDs<-cbind(D1,D2,D3,D4,D5,D6,D7,D8,D9,D10,D11,D12,D13,D14,D15) E1<-sum(Column1 %in% "E")/(length(Column1)-spaces1) E2<-sum(Column2 %in% "E")/(length(Column2)-spaces2) E3<-sum(Column3 %in% "E")/(length(Column3)-spaces3) E4<-sum(Column4 %in% "E")/(length(Column4)-spaces4) E5<-sum(Column5 %in% "E")/(length(Column5)-spaces5) E6<-sum(Column6 %in% "E")/(length(Column6)-spaces6) E7<-sum(Column7 %in% "E")/(length(Column7)-spaces7) E8<-sum(Column8 %in% "E")/(length(Column8)-spaces8) E9<-sum(Column9 %in% "E")/(length(Column9)-spaces9) E10<-sum(Column10 %in% "E")/(length(Column10)-spaces10) E11<-sum(Column11 %in% "E")/(length(Column11)-spaces11) E12<-sum(Column12 %in% "E")/(length(Column12)-spaces12) E13<-sum(Column13 %in% "E")/(length(Column13)-spaces13) E14<-sum(Column14 %in% "E")/(length(Column14)-spaces14) E15<-sum(Column15 %in% "E")/(length(Column15)-spaces15) EllEs<-cbind(E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,E13,E14,E15) F1<-sum(Column1 %in% "F")/(length(Column1)-spaces1) F2<-sum(Column2 %in% "F")/(length(Column2)-spaces2) F3<-sum(Column3 %in% "F")/(length(Column3)-spaces3) F4<-sum(Column4 %in% "F")/(length(Column4)-spaces4) F5<-sum(Column5 %in% "F")/(length(Column5)-spaces5) F6<-sum(Column6 %in% "F")/(length(Column6)-spaces6) F7<-sum(Column7 %in% "F")/(length(Column7)-spaces7) F8<-sum(Column8 %in% "F")/(length(Column8)-spaces8) F9<-sum(Column9 %in% "F")/(length(Column9)-spaces9) F10<-sum(Column10 %in% "F")/(length(Column10)-spaces10) F11<-sum(Column11 %in% "F")/(length(Column11)-spaces11) F12<-sum(Column12 %in% "F")/(length(Column12)-spaces12) F13<-sum(Column13 %in% "F")/(length(Column13)-spaces13) F14<-sum(Column14 %in% "F")/(length(Column14)-spaces14) F15<-sum(Column15 %in% "F")/(length(Column15)-spaces15) FllFs<-cbind(F1,F2,F3,F4,F5,F6,F7,F8,F9,F10,F11,F12,F13,F14,F15) G1<-sum(Column1 %in% "G")/(length(Column1)-spaces1) G2<-sum(Column2 %in% "G")/(length(Column2)-spaces2) G3<-sum(Column3 %in% "G")/(length(Column3)-spaces3) G4<-sum(Column4 %in% "G")/(length(Column4)-spaces4) G5<-sum(Column5 %in% "G")/(length(Column5)-spaces5) G6<-sum(Column6 %in% "G")/(length(Column6)-spaces6) G7<-sum(Column7 %in% "G")/(length(Column7)-spaces7) G8<-sum(Column8 %in% "G")/(length(Column8)-spaces8) G9<-sum(Column9 %in% "G")/(length(Column9)-spaces9) G10<-sum(Column10 %in% "G")/(length(Column10)-spaces10) G11<-sum(Column11 %in% "G")/(length(Column11)-spaces11) G12<-sum(Column12 %in% "G")/(length(Column12)-spaces12) G13<-sum(Column13 %in% "G")/(length(Column13)-spaces13) G14<-sum(Column14 %in% "G")/(length(Column14)-spaces14) G15<-sum(Column15 %in% "G")/(length(Column15)-spaces15) GllGs<-cbind(G1,G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,G13,G14,G15) H1<-sum(Column1 %in% "H")/(length(Column1)-spaces1) H2<-sum(Column2 %in% "H")/(length(Column2)-spaces2) H3<-sum(Column3 %in% "H")/(length(Column3)-spaces3) H4<-sum(Column4 %in% "H")/(length(Column4)-spaces4) H5<-sum(Column5 %in% "H")/(length(Column5)-spaces5) H6<-sum(Column6 %in% "H")/(length(Column6)-spaces6) H7<-sum(Column7 %in% "H")/(length(Column7)-spaces7) H8<-sum(Column8 %in% "H")/(length(Column8)-spaces8) H9<-sum(Column9 %in% "H")/(length(Column9)-spaces9) H10<-sum(Column10 %in% "H")/(length(Column10)-spaces10) H11<-sum(Column11 %in% "H")/(length(Column11)-spaces11) H12<-sum(Column12 %in% "H")/(length(Column12)-spaces12) H13<-sum(Column13 %in% "H")/(length(Column13)-spaces13) H14<-sum(Column14 %in% "H")/(length(Column14)-spaces14) H15<-sum(Column15 %in% "H")/(length(Column15)-spaces15) HllHs<-cbind(H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12,H13,H14,H15) I1<-sum(Column1 %in% "I")/(length(Column1)-spaces1) I2<-sum(Column2 %in% "I")/(length(Column2)-spaces2) I3<-sum(Column3 %in% "I")/(length(Column3)-spaces3) I4<-sum(Column4 %in% "I")/(length(Column4)-spaces4) I5<-sum(Column5 %in% "I")/(length(Column5)-spaces5) I6<-sum(Column6 %in% "I")/(length(Column6)-spaces6) I7<-sum(Column7 %in% "I")/(length(Column7)-spaces7) I8<-sum(Column8 %in% "I")/(length(Column8)-spaces8) I9<-sum(Column9 %in% "I")/(length(Column9)-spaces9) I10<-sum(Column10 %in% "I")/(length(Column10)-spaces10) I11<-sum(Column11 %in% "I")/(length(Column11)-spaces11) I12<-sum(Column12 %in% "I")/(length(Column12)-spaces12) I13<-sum(Column13 %in% "I")/(length(Column13)-spaces13) I14<-sum(Column14 %in% "I")/(length(Column14)-spaces14) I15<-sum(Column15 %in% "I")/(length(Column15)-spaces15) IllIs<-cbind(I1,I2,I3,I4,I5,I6,I7,I8,I9,I10,I11,I12,I13,I14,I15) K1<-sum(Column1 %in% "K")/(length(Column1)-spaces1) K2<-sum(Column2 %in% "K")/(length(Column2)-spaces2) K3<-sum(Column3 %in% "K")/(length(Column3)-spaces3) K4<-sum(Column4 %in% "K")/(length(Column4)-spaces4) K5<-sum(Column5 %in% "K")/(length(Column5)-spaces5) K6<-sum(Column6 %in% "K")/(length(Column6)-spaces6) K7<-sum(Column7 %in% "K")/(length(Column7)-spaces7) K8<-sum(Column8 %in% "K")/(length(Column8)-spaces8) K9<-sum(Column9 %in% "K")/(length(Column9)-spaces9) K10<-sum(Column10 %in% "K")/(length(Column10)-spaces10) K11<-sum(Column11 %in% "K")/(length(Column11)-spaces11) K12<-sum(Column12 %in% "K")/(length(Column12)-spaces12) K13<-sum(Column13 %in% "K")/(length(Column13)-spaces13) K14<-sum(Column14 %in% "K")/(length(Column14)-spaces14) K15<-sum(Column15 %in% "K")/(length(Column15)-spaces15) KllKs<-cbind(K1,K2,K3,K4,K5,K6,K7,K8,K9,K10,K11,K12,K13,K14,K15) L1<-sum(Column1 %in% "L")/(length(Column1)-spaces1) L2<-sum(Column2 %in% "L")/(length(Column2)-spaces2) L3<-sum(Column3 %in% "L")/(length(Column3)-spaces3) L4<-sum(Column4 %in% "L")/(length(Column4)-spaces4) L5<-sum(Column5 %in% "L")/(length(Column5)-spaces5) L6<-sum(Column6 %in% "L")/(length(Column6)-spaces6) L7<-sum(Column7 %in% "L")/(length(Column7)-spaces7) L8<-sum(Column8 %in% "L")/(length(Column8)-spaces8) L9<-sum(Column9 %in% "L")/(length(Column9)-spaces9) L10<-sum(Column10 %in% "L")/(length(Column10)-spaces10) L11<-sum(Column11 %in% "L")/(length(Column11)-spaces11) L12<-sum(Column12 %in% "L")/(length(Column12)-spaces12) L13<-sum(Column13 %in% "L")/(length(Column13)-spaces13) L14<-sum(Column14 %in% "L")/(length(Column14)-spaces14) L15<-sum(Column15 %in% "L")/(length(Column15)-spaces15) LllLs<-cbind(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L13,L14,L15) M1<-sum(Column1 %in% "M")/(length(Column1)-spaces1) M2<-sum(Column2 %in% "M")/(length(Column2)-spaces2) M3<-sum(Column3 %in% "M")/(length(Column3)-spaces3) M4<-sum(Column4 %in% "M")/(length(Column4)-spaces4) M5<-sum(Column5 %in% "M")/(length(Column5)-spaces5) M6<-sum(Column6 %in% "M")/(length(Column6)-spaces6) M7<-sum(Column7 %in% "M")/(length(Column7)-spaces7) M8<-sum(Column8 %in% "M")/(length(Column8)-spaces8) M9<-sum(Column9 %in% "M")/(length(Column9)-spaces9) M10<-sum(Column10 %in% "M")/(length(Column10)-spaces10) M11<-sum(Column11 %in% "M")/(length(Column11)-spaces11) M12<-sum(Column12 %in% "M")/(length(Column12)-spaces12) M13<-sum(Column13 %in% "M")/(length(Column13)-spaces13) M14<-sum(Column14 %in% "M")/(length(Column14)-spaces14) M15<-sum(Column15 %in% "M")/(length(Column15)-spaces15) MllMs<-cbind(M1,M2,M3,M4,M5,M6,M7,M8,M9,M10,M11,M12,M13,M14,M15) N1<-sum(Column1 %in% "N")/(length(Column1)-spaces1) N2<-sum(Column2 %in% "N")/(length(Column2)-spaces2) N3<-sum(Column3 %in% "N")/(length(Column3)-spaces3) N4<-sum(Column4 %in% "N")/(length(Column4)-spaces4) N5<-sum(Column5 %in% "N")/(length(Column5)-spaces5) N6<-sum(Column6 %in% "N")/(length(Column6)-spaces6) N7<-sum(Column7 %in% "N")/(length(Column7)-spaces7) N8<-sum(Column8 %in% "N")/(length(Column8)-spaces8) N9<-sum(Column9 %in% "N")/(length(Column9)-spaces9) N10<-sum(Column10 %in% "N")/(length(Column10)-spaces10) N11<-sum(Column11 %in% "N")/(length(Column11)-spaces11) N12<-sum(Column12 %in% "N")/(length(Column12)-spaces12) N13<-sum(Column13 %in% "N")/(length(Column13)-spaces13) N14<-sum(Column14 %in% "N")/(length(Column14)-spaces14) N15<-sum(Column15 %in% "N")/(length(Column15)-spaces15) NllNs<-cbind(N1,N2,N3,N4,N5,N6,N7,N8,N9,N10,N11,N12,N13,N14,N15) P1<-sum(Column1 %in% "P")/(length(Column1)-spaces1) P2<-sum(Column2 %in% "P")/(length(Column2)-spaces2) P3<-sum(Column3 %in% "P")/(length(Column3)-spaces3) P4<-sum(Column4 %in% "P")/(length(Column4)-spaces4) P5<-sum(Column5 %in% "P")/(length(Column5)-spaces5) P6<-sum(Column6 %in% "P")/(length(Column6)-spaces6) P7<-sum(Column7 %in% "P")/(length(Column7)-spaces7) P8<-sum(Column8 %in% "P")/(length(Column8)-spaces8) P9<-sum(Column9 %in% "P")/(length(Column9)-spaces9) P10<-sum(Column10 %in% "P")/(length(Column10)-spaces10) P11<-sum(Column11 %in% "P")/(length(Column11)-spaces11) P12<-sum(Column12 %in% "P")/(length(Column12)-spaces12) P13<-sum(Column13 %in% "P")/(length(Column13)-spaces13) P14<-sum(Column14 %in% "P")/(length(Column14)-spaces14) P15<-sum(Column15 %in% "P")/(length(Column15)-spaces15) PllPs<-cbind(P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15) Q1<-sum(Column1 %in% "Q")/(length(Column1)-spaces1) Q2<-sum(Column2 %in% "Q")/(length(Column2)-spaces2) Q3<-sum(Column3 %in% "Q")/(length(Column3)-spaces3) Q4<-sum(Column4 %in% "Q")/(length(Column4)-spaces4) Q5<-sum(Column5 %in% "Q")/(length(Column5)-spaces5) Q6<-sum(Column6 %in% "Q")/(length(Column6)-spaces6) Q7<-sum(Column7 %in% "Q")/(length(Column7)-spaces7) Q8<-sum(Column8 %in% "Q")/(length(Column8)-spaces8) Q9<-sum(Column9 %in% "Q")/(length(Column9)-spaces9) Q10<-sum(Column10 %in% "Q")/(length(Column10)-spaces10) Q11<-sum(Column11 %in% "Q")/(length(Column11)-spaces11) Q12<-sum(Column12 %in% "Q")/(length(Column12)-spaces12) Q13<-sum(Column13 %in% "Q")/(length(Column13)-spaces13) Q14<-sum(Column14 %in% "Q")/(length(Column14)-spaces14) Q15<-sum(Column15 %in% "Q")/(length(Column15)-spaces15) QllQs<-cbind(Q1,Q2,Q3,Q4,Q5,Q6,Q7,Q8,Q9,Q10,Q11,Q12,Q13,Q14,Q15) R1<-sum(Column1 %in% "R")/(length(Column1)-spaces1) R2<-sum(Column2 %in% "R")/(length(Column2)-spaces2) R3<-sum(Column3 %in% "R")/(length(Column3)-spaces3) R4<-sum(Column4 %in% "R")/(length(Column4)-spaces4) R5<-sum(Column5 %in% "R")/(length(Column5)-spaces5) R6<-sum(Column6 %in% "R")/(length(Column6)-spaces6) R7<-sum(Column7 %in% "R")/(length(Column7)-spaces7) R8<-sum(Column8 %in% "R")/(length(Column8)-spaces8) R9<-sum(Column9 %in% "R")/(length(Column9)-spaces9) R10<-sum(Column10 %in% "R")/(length(Column10)-spaces10) R11<-sum(Column11 %in% "R")/(length(Column11)-spaces11) R12<-sum(Column12 %in% "R")/(length(Column12)-spaces12) R13<-sum(Column13 %in% "R")/(length(Column13)-spaces13) R14<-sum(Column14 %in% "R")/(length(Column14)-spaces14) R15<-sum(Column15 %in% "R")/(length(Column15)-spaces15) RllRs<-cbind(R1,R2,R3,R4,R5,R6,R7,R8,R9,R10,R11,R12,R13,R14,R15) S1<-sum(Column1 %in% "S")/(length(Column1)-spaces1) S2<-sum(Column2 %in% "S")/(length(Column2)-spaces2) S3<-sum(Column3 %in% "S")/(length(Column3)-spaces3) S4<-sum(Column4 %in% "S")/(length(Column4)-spaces4) S5<-sum(Column5 %in% "S")/(length(Column5)-spaces5) S6<-sum(Column6 %in% "S")/(length(Column6)-spaces6) S7<-sum(Column7 %in% "S")/(length(Column7)-spaces7) S8<-sum(Column8 %in% "S")/(length(Column8)-spaces8) S9<-sum(Column9 %in% "S")/(length(Column9)-spaces9) S10<-sum(Column10 %in% "S")/(length(Column10)-spaces10) S11<-sum(Column11 %in% "S")/(length(Column11)-spaces11) S12<-sum(Column12 %in% "S")/(length(Column12)-spaces12) S13<-sum(Column13 %in% "S")/(length(Column13)-spaces13) S14<-sum(Column14 %in% "S")/(length(Column14)-spaces14) S15<-sum(Column15 %in% "S")/(length(Column15)-spaces15) SllSs<-cbind(S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15) T1<-sum(Column1 %in% "T")/(length(Column1)-spaces1) T2<-sum(Column2 %in% "T")/(length(Column2)-spaces2) T3<-sum(Column3 %in% "T")/(length(Column3)-spaces3) T4<-sum(Column4 %in% "T")/(length(Column4)-spaces4) T5<-sum(Column5 %in% "T")/(length(Column5)-spaces5) T6<-sum(Column6 %in% "T")/(length(Column6)-spaces6) T7<-sum(Column7 %in% "T")/(length(Column7)-spaces7) T8<-sum(Column8 %in% "T")/(length(Column8)-spaces8) T9<-sum(Column9 %in% "T")/(length(Column9)-spaces9) T10<-sum(Column10 %in% "T")/(length(Column10)-spaces10) T11<-sum(Column11 %in% "T")/(length(Column11)-spaces11) T12<-sum(Column12 %in% "T")/(length(Column12)-spaces12) T13<-sum(Column13 %in% "T")/(length(Column13)-spaces13) T14<-sum(Column14 %in% "T")/(length(Column14)-spaces14) T15<-sum(Column15 %in% "T")/(length(Column15)-spaces15) TllTs<-cbind(T1,T2,T3,T4,T5,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15) V1<-sum(Column1 %in% "V")/(length(Column1)-spaces1) V2<-sum(Column2 %in% "V")/(length(Column2)-spaces2) V3<-sum(Column3 %in% "V")/(length(Column3)-spaces3) V4<-sum(Column4 %in% "V")/(length(Column4)-spaces4) V5<-sum(Column5 %in% "V")/(length(Column5)-spaces5) V6<-sum(Column6 %in% "V")/(length(Column6)-spaces6) V7<-sum(Column7 %in% "V")/(length(Column7)-spaces7) V8<-sum(Column8 %in% "V")/(length(Column8)-spaces8) V9<-sum(Column9 %in% "V")/(length(Column9)-spaces9) V10<-sum(Column10 %in% "V")/(length(Column10)-spaces10) V11<-sum(Column11 %in% "V")/(length(Column11)-spaces11) V12<-sum(Column12 %in% "V")/(length(Column12)-spaces12) V13<-sum(Column13 %in% "V")/(length(Column13)-spaces13) V14<-sum(Column14 %in% "V")/(length(Column14)-spaces14) V15<-sum(Column15 %in% "V")/(length(Column15)-spaces15) VllVs<-cbind(V1,V2,V3,V4,V5,V6,V7,V8,V9,V10,V11,V12,V13,V14,V15) W1<-sum(Column1 %in% "W")/(length(Column1)-spaces1) W2<-sum(Column2 %in% "W")/(length(Column2)-spaces2) W3<-sum(Column3 %in% "W")/(length(Column3)-spaces3) W4<-sum(Column4 %in% "W")/(length(Column4)-spaces4) W5<-sum(Column5 %in% "W")/(length(Column5)-spaces5) W6<-sum(Column6 %in% "W")/(length(Column6)-spaces6) W7<-sum(Column7 %in% "W")/(length(Column7)-spaces7) W8<-sum(Column8 %in% "W")/(length(Column8)-spaces8) W9<-sum(Column9 %in% "W")/(length(Column9)-spaces9) W10<-sum(Column10 %in% "W")/(length(Column10)-spaces10) W11<-sum(Column11 %in% "W")/(length(Column11)-spaces11) W12<-sum(Column12 %in% "W")/(length(Column12)-spaces12) W13<-sum(Column13 %in% "W")/(length(Column13)-spaces13) W14<-sum(Column14 %in% "W")/(length(Column14)-spaces14) W15<-sum(Column15 %in% "W")/(length(Column15)-spaces15) WllWs<-cbind(W1,W2,W3,W4,W5,W6,W7,W8,W9,W10,W11,W12,W13,W14,W15) Y1<-sum(Column1 %in% "Y")/(length(Column1)-spaces1) Y2<-sum(Column2 %in% "Y")/(length(Column2)-spaces2) Y3<-sum(Column3 %in% "Y")/(length(Column3)-spaces3) Y4<-sum(Column4 %in% "Y")/(length(Column4)-spaces4) Y5<-sum(Column5 %in% "Y")/(length(Column5)-spaces5) Y6<-sum(Column6 %in% "Y")/(length(Column6)-spaces6) Y7<-sum(Column7 %in% "Y")/(length(Column7)-spaces7) Y8<-sum(Column8 %in% "Y")/(length(Column8)-spaces8) Y9<-sum(Column9 %in% "Y")/(length(Column9)-spaces9) Y10<-sum(Column10 %in% "Y")/(length(Column10)-spaces10) Y11<-sum(Column11 %in% "Y")/(length(Column11)-spaces11) Y12<-sum(Column12 %in% "Y")/(length(Column12)-spaces12) Y13<-sum(Column13 %in% "Y")/(length(Column13)-spaces13) Y14<-sum(Column14 %in% "Y")/(length(Column14)-spaces14) Y15<-sum(Column15 %in% "Y")/(length(Column15)-spaces15) YllYs<-cbind(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14,Y15) } #this is substrate percents #A C D E F G H I K L N P Q R S T V W Y PercentTable<-rbind(AllAs,CllCs,DllDs,EllEs,FllFs,GllGs,HllHs,IllIs,KllKs,LllLs,MllMs,NllNs,PllPs,QllQs,RllRs,SllSs,TllTs,VllVs,WllWs,YllYs) PercentTable<-PercentTable*100 #create the SD table SDtable<-matrix(data = rep(1,times=(nrow(PercentTable)*ncol(PercentTable))),nrow = nrow(PercentTable),ncol = ncol(PercentTable)) #for every row, a percertage minus the same mean over the same SD if(1==1){ SDtable[1,]<-(PercentTable[1,]-Amean)/Asd SDtable[2,]<-(PercentTable[2,]-Cmean)/Csd SDtable[3,]<-(PercentTable[3,]-Dmean)/Dsd SDtable[4,]<-(PercentTable[4,]-Emean)/Esd SDtable[5,]<-(PercentTable[5,]-Fmean)/Fsd SDtable[6,]<-(PercentTable[6,]-Gmean)/Gsd SDtable[7,]<-(PercentTable[7,]-Hmean)/Hsd SDtable[8,]<-(PercentTable[8,]-Imean)/Isd SDtable[9,]<-(PercentTable[9,]-Kmean)/Ksd SDtable[10,]<-(PercentTable[10,]-Lmean)/Lsd SDtable[11,]<-(PercentTable[11,]-Mmean)/Msd SDtable[12,]<-(PercentTable[12,]-Nmean)/Nsd SDtable[13,]<-(PercentTable[13,]-Pmean)/Psd SDtable[14,]<-(PercentTable[14,]-Qmean)/Qsd SDtable[15,]<-(PercentTable[15,]-Rmean)/Rsd SDtable[16,]<-(PercentTable[16,]-Smean)/Ssd SDtable[17,]<-(PercentTable[17,]-Tmean)/Tsd SDtable[18,]<-(PercentTable[18,]-Vmean)/Vsd SDtable[19,]<-(PercentTable[19,]-Wmean)/Wsd SDtable[20,]<-(PercentTable[20,]-Ymean)/Ysd } SetOfAAs<-c("Letter","A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y") SumOfSigmaAAs<-c(1:15) for (i in 1:15){ SumOfSigmasValue<-0 for (j in 1:20){ value<-0 if (SDtable[j,i]>2){ value<-sum(substrates[,i]==SetOfAAs[j]) } SumOfSigmasValue<-SumOfSigmasValue+value } SumOfSigmaAAs[i]<-SumOfSigmasValue } # AAs1<-length(substrates[,1])-sum(substrates[,1]=="") # AAs2<-length(substrates[,2])-sum(substrates[,2]=="") # AAs3<-length(substrates[,3])-sum(substrates[,3]=="") # AAs4<-length(substrates[,4])-sum(substrates[,4]=="") # AAs5<-length(substrates[,5])-sum(substrates[,5]=="") # AAs6<-length(substrates[,6])-sum(substrates[,6]=="") # AAs7<-length(substrates[,7])-sum(substrates[,7]=="") # AAs8<-length(substrates[,8])-sum(substrates[,8]=="") # AAs9<-length(substrates[,9])-sum(substrates[,9]=="") # # # # #AAsAtPositions<-c(AAs1,AAs2,AAs3,AAs4,AAs5,AAs6,AAs7,AAs8,AAs9) # AAsAtPositions<-c(length(substrates[,1]),length(substrates[,2]),length(substrates[,3]),length(substrates[,4]), # length(substrates[,5]),length(substrates[,6]),length(substrates[,7]),length(substrates[,8]), # length(substrates[,9])) SumOfExpectedSigmaAAs<-c(1:15) for (i in 1:15){ ExpectedValue<-0 for (j in 1:20){ value<-0 if (SDtable[j,i]>2){ value<-AllMeans[j] } ExpectedValue<-ExpectedValue+value } SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100 } SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow) SetOfAAs<-matrix(data = SetOfAAs,ncol = 1) SDtableu<-SDtable HeaderSD<-c(-7:7) SDtable<-rbind(HeaderSD,SDtableu) row.names(SDtable)<-NULL SDtable<-data.frame(SetOfAAs,SDtable) PercentTable<-rbind(HeaderSD,PercentTable) row.names(PercentTable)<-NULL PercentTable<-data.frame(SetOfAAs,PercentTable) numberofY<-as.numeric(SubstrateBackgroundFrequency$Number.of.Y) numberofY<-numberofY[!is.na(numberofY)] numberofPY<-as.numeric(SubstrateBackgroundFrequency$Number.of.pY) numberofPY<-numberofPY[!is.na(numberofPY)] NormalizationScore<-sum(numberofPY)/sum(numberofY) # positions<-matrix(data = NA, nrow=20,ncol = 15) # # #column1 # # for (q in 1:15) { # sA<-sum(substrates[,i]=="A") # positions[1,i]<-sA # sC<-sum(substrates[,i]=="C") # positions[2,i]<-sC # sD<-sum(substrates[,i]=="D") # positions[3,i]<-sD # sE<-sum(substrates[,i]=="E") # positions[4,i]<-sE # sF<-sum(substrates[,i]=="F") # sG<-sum(substrates[,i]=="G") # sH<-sum(substrates[,i]=="H") # sI<-sum(substrates[,i]=="I") # sK<-sum(substrates[,i]=="K") # sL<-sum(substrates[,i]=="L") # sM<-sum(substrates[,i]=="M") # sN<-sum(substrates[,i]=="N") # sP<-sum(substrates[,i]=="P") # sQ<-sum(substrates[,i]=="Q") # sR<-sum(substrates[,i]=="R") # sS<-sum(substrates[,i]=="S") # sT<-sum(substrates[,i]=="T") # sV<-sum(substrates[,i]=="V") # sW<-sum(substrates[,i]=="W") # sY<-sum(substrates[,i]=="Y") # positions[5,i]<-sF # positions[6,i]<-sG # positions[7,i]<-sH # positions[8,i]<-sI # positions[9,i]<-sK # positions[10,i]<-sL # positions[11,i]<-sM # positions[12,i]<-sN # positions[13,i]<-sP # positions[14,i]<-sQ # positions[15,i]<-sR # positions[16,i]<-sS # positions[17,i]<-sT # positions[18,i]<-sV # positions[19,i]<-sW # positions[20,i]<-sY # } #here I create the positions table which is needed for the endogenous prob matrix and is simply "how many times did an AA show up in this spot? if (6==6){ Column1<-substrates[,1] Column2<-substrates[,2] Column3<-substrates[,3] Column4<-substrates[,4] Column5<-substrates[,5] Column6<-substrates[,6] Column7<-substrates[,7] Column8<-substrates[,8] Column9<-substrates[,9] Column10<-substrates[,10] Column11<-substrates[,11] Column12<-substrates[,12] Column13<-substrates[,13] Column14<-substrates[,14] Column15<-substrates[,15] spaces1<-sum((Column1%in% "")) spaces2<-sum(Column2%in% "") spaces3<-sum(Column3%in% "") spaces4<-sum(Column4%in% "") spaces5<-sum(Column5%in% "") spaces6<-sum(Column6%in% "") spaces7<-sum(Column7%in% "") spaces8<-sum(Column8%in% "") spaces9<-sum(Column9%in% "") spaces10<-sum(Column10%in% "") spaces11<-sum(Column11%in% "") spaces12<-sum(Column12%in% "") spaces13<-sum(Column13%in% "") spaces14<-sum(Column14%in% "") spaces15<-sum(Column15%in% "") A1<-sum(Column1 %in% "A") A2<-sum(Column2 %in% "A") A3<-sum(Column3 %in% "A") A4<-sum(Column4 %in% "A") A5<-sum(Column5 %in% "A") A6<-sum(Column6 %in% "A") A7<-sum(Column7 %in% "A") A8<-sum(Column8 %in% "A") A9<-sum(Column9 %in% "A") A10<-sum(Column10 %in% "A") A11<-sum(Column11 %in% "A") A12<-sum(Column12 %in% "A") A13<-sum(Column13 %in% "A") A14<-sum(Column14 %in% "A") A15<-sum(Column15 %in% "A") AllAs<-cbind(A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,A13,A14,A15) C1<-sum(Column1 %in% "C") C2<-sum(Column2 %in% "C") C3<-sum(Column3 %in% "C") C4<-sum(Column4 %in% "C") C5<-sum(Column5 %in% "C") C6<-sum(Column6 %in% "C") C7<-sum(Column7 %in% "C") C8<-sum(Column8 %in% "C") C9<-sum(Column9 %in% "C") C10<-sum(Column10 %in% "C") C11<-sum(Column11 %in% "C") C12<-sum(Column12 %in% "C") C13<-sum(Column13 %in% "C") C14<-sum(Column14 %in% "C") C15<-sum(Column15 %in% "C") CllCs<-cbind(C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,C13,C14,C15) D1<-sum(Column1 %in% "D") D2<-sum(Column2 %in% "D") D3<-sum(Column3 %in% "D") D4<-sum(Column4 %in% "D") D5<-sum(Column5 %in% "D") D6<-sum(Column6 %in% "D") D7<-sum(Column7 %in% "D") D8<-sum(Column8 %in% "D") D9<-sum(Column9 %in% "D") D10<-sum(Column10 %in% "D") D11<-sum(Column11 %in% "D") D12<-sum(Column12 %in% "D") D13<-sum(Column13 %in% "D") D14<-sum(Column14 %in% "D") D15<-sum(Column15 %in% "D") DllDs<-cbind(D1,D2,D3,D4,D5,D6,D7,D8,D9,D10,D11,D12,D13,D14,D15) E1<-sum(Column1 %in% "E") E2<-sum(Column2 %in% "E") E3<-sum(Column3 %in% "E") E4<-sum(Column4 %in% "E") E5<-sum(Column5 %in% "E") E6<-sum(Column6 %in% "E") E7<-sum(Column7 %in% "E") E8<-sum(Column8 %in% "E") E9<-sum(Column9 %in% "E") E10<-sum(Column10 %in% "E") E11<-sum(Column11 %in% "E") E12<-sum(Column12 %in% "E") E13<-sum(Column13 %in% "E") E14<-sum(Column14 %in% "E") E15<-sum(Column15 %in% "E") EllEs<-cbind(E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,E13,E14,E15) F1<-sum(Column1 %in% "F") F2<-sum(Column2 %in% "F") F3<-sum(Column3 %in% "F") F4<-sum(Column4 %in% "F") F5<-sum(Column5 %in% "F") F6<-sum(Column6 %in% "F") F7<-sum(Column7 %in% "F") F8<-sum(Column8 %in% "F") F9<-sum(Column9 %in% "F") F10<-sum(Column10 %in% "F") F11<-sum(Column11 %in% "F") F12<-sum(Column12 %in% "F") F13<-sum(Column13 %in% "F") F14<-sum(Column14 %in% "F") F15<-sum(Column15 %in% "F") FllFs<-cbind(F1,F2,F3,F4,F5,F6,F7,F8,F9,F10,F11,F12,F13,F14,F15) G1<-sum(Column1 %in% "G") G2<-sum(Column2 %in% "G") G3<-sum(Column3 %in% "G") G4<-sum(Column4 %in% "G") G5<-sum(Column5 %in% "G") G6<-sum(Column6 %in% "G") G7<-sum(Column7 %in% "G") G8<-sum(Column8 %in% "G") G9<-sum(Column9 %in% "G") G10<-sum(Column10 %in% "G") G11<-sum(Column11 %in% "G") G12<-sum(Column12 %in% "G") G13<-sum(Column13 %in% "G") G14<-sum(Column14 %in% "G") G15<-sum(Column15 %in% "G") GllGs<-cbind(G1,G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,G13,G14,G15) H1<-sum(Column1 %in% "H") H2<-sum(Column2 %in% "H") H3<-sum(Column3 %in% "H") H4<-sum(Column4 %in% "H") H5<-sum(Column5 %in% "H") H6<-sum(Column6 %in% "H") H7<-sum(Column7 %in% "H") H8<-sum(Column8 %in% "H") H9<-sum(Column9 %in% "H") H10<-sum(Column10 %in% "H") H11<-sum(Column11 %in% "H") H12<-sum(Column12 %in% "H") H13<-sum(Column13 %in% "H") H14<-sum(Column14 %in% "H") H15<-sum(Column15 %in% "H") HllHs<-cbind(H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12,H13,H14,H15) I1<-sum(Column1 %in% "I") I2<-sum(Column2 %in% "I") I3<-sum(Column3 %in% "I") I4<-sum(Column4 %in% "I") I5<-sum(Column5 %in% "I") I6<-sum(Column6 %in% "I") I7<-sum(Column7 %in% "I") I8<-sum(Column8 %in% "I") I9<-sum(Column9 %in% "I") I10<-sum(Column10 %in% "I") I11<-sum(Column11 %in% "I") I12<-sum(Column12 %in% "I") I13<-sum(Column13 %in% "I") I14<-sum(Column14 %in% "I") I15<-sum(Column15 %in% "I") IllIs<-cbind(I1,I2,I3,I4,I5,I6,I7,I8,I9,I10,I11,I12,I13,I14,I15) K1<-sum(Column1 %in% "K") K2<-sum(Column2 %in% "K") K3<-sum(Column3 %in% "K") K4<-sum(Column4 %in% "K") K5<-sum(Column5 %in% "K") K6<-sum(Column6 %in% "K") K7<-sum(Column7 %in% "K") K8<-sum(Column8 %in% "K") K9<-sum(Column9 %in% "K") K10<-sum(Column10 %in% "K") K11<-sum(Column11 %in% "K") K12<-sum(Column12 %in% "K") K13<-sum(Column13 %in% "K") K14<-sum(Column14 %in% "K") K15<-sum(Column15 %in% "K") KllKs<-cbind(K1,K2,K3,K4,K5,K6,K7,K8,K9,K10,K11,K12,K13,K14,K15) L1<-sum(Column1 %in% "L") L2<-sum(Column2 %in% "L") L3<-sum(Column3 %in% "L") L4<-sum(Column4 %in% "L") L5<-sum(Column5 %in% "L") L6<-sum(Column6 %in% "L") L7<-sum(Column7 %in% "L") L8<-sum(Column8 %in% "L") L9<-sum(Column9 %in% "L") L10<-sum(Column10 %in% "L") L11<-sum(Column11 %in% "L") L12<-sum(Column12 %in% "L") L13<-sum(Column13 %in% "L") L14<-sum(Column14 %in% "L") L15<-sum(Column15 %in% "L") LllLs<-cbind(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L13,L14,L15) M1<-sum(Column1 %in% "M") M2<-sum(Column2 %in% "M") M3<-sum(Column3 %in% "M") M4<-sum(Column4 %in% "M") M5<-sum(Column5 %in% "M") M6<-sum(Column6 %in% "M") M7<-sum(Column7 %in% "M") M8<-sum(Column8 %in% "M") M9<-sum(Column9 %in% "M") M10<-sum(Column10 %in% "M") M11<-sum(Column11 %in% "M") M12<-sum(Column12 %in% "M") M13<-sum(Column13 %in% "M") M14<-sum(Column14 %in% "M") M15<-sum(Column15 %in% "M") MllMs<-cbind(M1,M2,M3,M4,M5,M6,M7,M8,M9,M10,M11,M12,M13,M14,M15) N1<-sum(Column1 %in% "N") N2<-sum(Column2 %in% "N") N3<-sum(Column3 %in% "N") N4<-sum(Column4 %in% "N") N5<-sum(Column5 %in% "N") N6<-sum(Column6 %in% "N") N7<-sum(Column7 %in% "N") N8<-sum(Column8 %in% "N") N9<-sum(Column9 %in% "N") N10<-sum(Column10 %in% "N") N11<-sum(Column11 %in% "N") N12<-sum(Column12 %in% "N") N13<-sum(Column13 %in% "N") N14<-sum(Column14 %in% "N") N15<-sum(Column15 %in% "N") NllNs<-cbind(N1,N2,N3,N4,N5,N6,N7,N8,N9,N10,N11,N12,N13,N14,N15) P1<-sum(Column1 %in% "P") P2<-sum(Column2 %in% "P") P3<-sum(Column3 %in% "P") P4<-sum(Column4 %in% "P") P5<-sum(Column5 %in% "P") P6<-sum(Column6 %in% "P") P7<-sum(Column7 %in% "P") P8<-sum(Column8 %in% "P") P9<-sum(Column9 %in% "P") P10<-sum(Column10 %in% "P") P11<-sum(Column11 %in% "P") P12<-sum(Column12 %in% "P") P13<-sum(Column13 %in% "P") P14<-sum(Column14 %in% "P") P15<-sum(Column15 %in% "P") PllPs<-cbind(P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15) Q1<-sum(Column1 %in% "Q") Q2<-sum(Column2 %in% "Q") Q3<-sum(Column3 %in% "Q") Q4<-sum(Column4 %in% "Q") Q5<-sum(Column5 %in% "Q") Q6<-sum(Column6 %in% "Q") Q7<-sum(Column7 %in% "Q") Q8<-sum(Column8 %in% "Q") Q9<-sum(Column9 %in% "Q") Q10<-sum(Column10 %in% "Q") Q11<-sum(Column11 %in% "Q") Q12<-sum(Column12 %in% "Q") Q13<-sum(Column13 %in% "Q") Q14<-sum(Column14 %in% "Q") Q15<-sum(Column15 %in% "Q") QllQs<-cbind(Q1,Q2,Q3,Q4,Q5,Q6,Q7,Q8,Q9,Q10,Q11,Q12,Q13,Q14,Q15) R1<-sum(Column1 %in% "R") R2<-sum(Column2 %in% "R") R3<-sum(Column3 %in% "R") R4<-sum(Column4 %in% "R") R5<-sum(Column5 %in% "R") R6<-sum(Column6 %in% "R") R7<-sum(Column7 %in% "R") R8<-sum(Column8 %in% "R") R9<-sum(Column9 %in% "R") R10<-sum(Column10 %in% "R") R11<-sum(Column11 %in% "R") R12<-sum(Column12 %in% "R") R13<-sum(Column13 %in% "R") R14<-sum(Column14 %in% "R") R15<-sum(Column15 %in% "R") RllRs<-cbind(R1,R2,R3,R4,R5,R6,R7,R8,R9,R10,R11,R12,R13,R14,R15) S1<-sum(Column1 %in% "S") S2<-sum(Column2 %in% "S") S3<-sum(Column3 %in% "S") S4<-sum(Column4 %in% "S") S5<-sum(Column5 %in% "S") S6<-sum(Column6 %in% "S") S7<-sum(Column7 %in% "S") S8<-sum(Column8 %in% "S") S9<-sum(Column9 %in% "S") S10<-sum(Column10 %in% "S") S11<-sum(Column11 %in% "S") S12<-sum(Column12 %in% "S") S13<-sum(Column13 %in% "S") S14<-sum(Column14 %in% "S") S15<-sum(Column15 %in% "S") SllSs<-cbind(S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15) T1<-sum(Column1 %in% "T") T2<-sum(Column2 %in% "T") T3<-sum(Column3 %in% "T") T4<-sum(Column4 %in% "T") T5<-sum(Column5 %in% "T") T6<-sum(Column6 %in% "T") T7<-sum(Column7 %in% "T") T8<-sum(Column8 %in% "T") T9<-sum(Column9 %in% "T") T10<-sum(Column10 %in% "T") T11<-sum(Column11 %in% "T") T12<-sum(Column12 %in% "T") T13<-sum(Column13 %in% "T") T14<-sum(Column14 %in% "T") T15<-sum(Column15 %in% "T") TllTs<-cbind(T1,T2,T3,T4,T5,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15) V1<-sum(Column1 %in% "V") V2<-sum(Column2 %in% "V") V3<-sum(Column3 %in% "V") V4<-sum(Column4 %in% "V") V5<-sum(Column5 %in% "V") V6<-sum(Column6 %in% "V") V7<-sum(Column7 %in% "V") V8<-sum(Column8 %in% "V") V9<-sum(Column9 %in% "V") V10<-sum(Column10 %in% "V") V11<-sum(Column11 %in% "V") V12<-sum(Column12 %in% "V") V13<-sum(Column13 %in% "V") V14<-sum(Column14 %in% "V") V15<-sum(Column15 %in% "V") VllVs<-cbind(V1,V2,V3,V4,V5,V6,V7,V8,V9,V10,V11,V12,V13,V14,V15) W1<-sum(Column1 %in% "W") W2<-sum(Column2 %in% "W") W3<-sum(Column3 %in% "W") W4<-sum(Column4 %in% "W") W5<-sum(Column5 %in% "W") W6<-sum(Column6 %in% "W") W7<-sum(Column7 %in% "W") W8<-sum(Column8 %in% "W") W9<-sum(Column9 %in% "W") W10<-sum(Column10 %in% "W") W11<-sum(Column11 %in% "W") W12<-sum(Column12 %in% "W") W13<-sum(Column13 %in% "W") W14<-sum(Column14 %in% "W") W15<-sum(Column15 %in% "W") WllWs<-cbind(W1,W2,W3,W4,W5,W6,W7,W8,W9,W10,W11,W12,W13,W14,W15) Y1<-sum(Column1 %in% "Y") Y2<-sum(Column2 %in% "Y") Y3<-sum(Column3 %in% "Y") Y4<-sum(Column4 %in% "Y") Y5<-sum(Column5 %in% "Y") Y6<-sum(Column6 %in% "Y") Y7<-sum(Column7 %in% "Y") Y8<-sum(Column8 %in% "Y") Y9<-sum(Column9 %in% "Y") Y10<-sum(Column10 %in% "Y") Y11<-sum(Column11 %in% "Y") Y12<-sum(Column12 %in% "Y") Y13<-sum(Column13 %in% "Y") Y14<-sum(Column14 %in% "Y") Y15<-sum(Column15 %in% "Y") YllYs<-cbind(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14,Y15) PositionTable<-rbind(AllAs,CllCs,DllDs,EllEs,FllFs,GllGs,HllHs,IllIs,KllKs,LllLs,MllMs,NllNs,PllPs,QllQs,RllRs,SllSs,TllTs,VllVs,WllWs,YllYs) } #endogenous prob matrix is AA position over subbackfreqmean dim(PositionTable) EPMtable<-PositionTable # EPMtable[1,]<-(PositionTable[1,]/(PositionTable[1,]*.01*Amean)) # EPMtable[2,]<-(PositionTable[2,]/(PositionTable[2,]*.01*Cmean)) # EPMtable[3,]<-(PositionTable[3,]/(PositionTable[3,]*.01*Dmean)) # EPMtable[4,]<-(PositionTable[4,]/(PositionTable[4,]*.01*Emean)) # EPMtable[5,]<-(PositionTable[5,]/(PositionTable[5,]*.01*Fmean)) # EPMtable[6,]<-(PositionTable[6,]/(PositionTable[6,]*.01*Gmean)) # EPMtable[7,]<-(PositionTable[7,]/(PositionTable[7,]*.01*Hmean)) # EPMtable[8,]<-(PositionTable[8,]/(PositionTable[8,]*.01*Imean)) # EPMtable[9,]<-(PositionTable[9,]/(PositionTable[9,]*.01*Kmean)) # EPMtable[10,]<-(PositionTable[10,]/(PositionTable[10,]*.01*Lmean)) # EPMtable[11,]<-(PositionTable[11,]/(PositionTable[11,]*.01*Mmean)) # EPMtable[12,]<-(PositionTable[12,]/(PositionTable[12,]*.01*Nmean)) # EPMtable[13,]<-(PositionTable[13,]/(PositionTable[13,]*.01*Pmean)) # EPMtable[14,]<-(PositionTable[14,]/(PositionTable[14,]*.01*Qmean)) # EPMtable[15,]<-(PositionTable[15,]/(PositionTable[15,]*.01*Rmean)) # EPMtable[16,]<-(PositionTable[16,]/(PositionTable[16,]*.01*Smean)) # EPMtable[17,]<-(PositionTable[17,]/(PositionTable[17,]*.01*Tmean)) # EPMtable[18,]<-(PositionTable[18,]/(PositionTable[18,]*.01*Vmean)) # EPMtable[19,]<-(PositionTable[19,]/(PositionTable[19,]*.01*Wmean)) # EPMtable[20,]<-(PositionTable[20,]/(PositionTable[20,]*.01*Ymean)) columns<-c(length(Column1)-sum(Column1==""), length(Column2)-sum(Column2==""), length(Column3)-sum(Column3==""), length(Column4)-sum(Column4==""), length(Column5)-sum(Column5==""), length(Column6)-sum(Column6==""), length(Column7)-sum(Column7==""), length(Column8)-sum(Column8==""), length(Column9)-sum(Column9==""), length(Column10)-sum(Column10==""), length(Column11)-sum(Column11==""), length(Column12)-sum(Column12==""), length(Column13)-sum(Column13==""), length(Column14)-sum(Column14==""), length(Column15)-sum(Column15=="")) for (z in 1:15) { for (y in 1:20) { if (PositionTable[y,z]>0){ EPMtable[y,z]<-PositionTable[y,z]/((columns[z]*.01*AllMeans[y])) } if (PositionTable[y,z]==0){ EPMtable[y,z]<-(1/columns[z])/((columns[z]*.01*AllMeans[y])) } } } #here I created the endogenous probability matrix #now all I need to do is make the program automatically determine which SDs are >2, and then make it perform screener and sorter on those SDs # write.xlsx(SDtable,file=FILENAME, sheetName = "Standard Deviation Table",col.names = FALSE,row.names = FALSE,append = TRUE) # write.xlsx(PercentTable,file = FILENAME,sheetName = "Percent Table",col.names = FALSE,row.names = FALSE,append = TRUE) # write.xlsx(SelectivitySheet,file = FILENAME,sheetName = "Site Selectivity",col.names = FALSE,row.names = FALSE,append = TRUE) # write.xlsx(EPMtable,file=FILENAME,sheetName = "Endogenous Probability Matrix",col.names = FALSE,row.names = FALSE,append = TRUE) # write.xlsx(NormalizationScore,file = FILENAME,sheetName = "Normalization Score",col.names = FALSE,row.names = FALSE,append = TRUE) NormalizationScore<-c("Normalization Score",NormalizationScore) write.table(x=c("SD Table"),file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) write.table(SDtable,file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) write.table(x=c("Percent Table"),file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) write.table(PercentTable,file=FILENAME, append = TRUE,sep=",",row.names = FALSE, col.names = FALSE) EPMtableu<-EPMtable HeaderSD<-c(-7:7) EPMtableu<-rbind(HeaderSD,EPMtableu) row.names(EPMtableu)<-NULL EPMtableu<-data.frame(SetOfAAs,EPMtableu) write.table("Site Selectivity Matrix", file = FILENAME2, append = TRUE, sep = ",", row.names = FALSE, col.names = FALSE) SelectivityHeader=matrix(data = c("Position",-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7),nrow = 1) head<-matrix(data=rep(" ",times=16),nrow = 1) SelectivityHeader<-rbind(head,SelectivityHeader) write.table(SelectivityHeader, file = FILENAME2, append = TRUE, sep = ",", row.names = FALSE, col.names = FALSE) #colnames(SelectivitySheet)<-c("-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7") write.table(SelectivitySheet,file = FILENAME2, append = TRUE,sep = ",",row.names = TRUE, col.names = FALSE) write.table(x=c("Endogenous Probability Matrix"),file=FILENAME2,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) write.table(EPMtableu,file = FILENAME2, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE) write.table(NormalizationScore, file = FILENAME2, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE)