annotate kinatestid_r/.Rhistory @ 20:f7a6a3ec7710 draft default tip

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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')