Mercurial > repos > jfb > kinatest_r_7_7testing
diff kinatestid_r/.Rhistory @ 18:e16ca3e9fc49 draft
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| author | jfb |
|---|---|
| date | Tue, 17 Apr 2018 13:07:41 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kinatestid_r/.Rhistory Tue Apr 17 13:07:41 2018 -0400 @@ -0,0 +1,512 @@ +SubstrateBackgroundFrequency<- read.csv("7to7PositiveSubBAckFreq_11-7-17.csv", stringsAsFactors=FALSE, header = FALSE) +ScreenerFilename<-"screener7-7.csv" +FILENAME<-"output1.csv" +FILENAME2<-"output2.csv" +FILENAME3<-"output3.csv" +SubstrateBackgroundFrequency<-t(SubstrateBackgroundFrequency) +# number<-nrow(SubstrateBackgroundFrequency)-1 +SubstrateBackgroundFrequency<-SubstrateBackgroundFrequency[2:nrow(SubstrateBackgroundFrequency),] +Sub<-na.omit(SubstrateBackgroundFrequency) +SubstrateBackgroundFrequency<-Sub +# +# args = commandArgs(trailingOnly=TRUE) +# TodaysKinase<-as.character(args[1]) +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) +SDtable +Amean +Cmean +Wsd +Amean +head(SubstrateBackgroundFrequency) +source('C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/KinatestSwitcheroo.R') +source('C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/KinatestSwitcheroo.R') +source('C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/KinatestSwitcheroo.R')