| Previous changeset 5:aff861ca6e2b (2019-01-14) Next changeset 7:77f3a77f0ca2 (2020-07-14) |
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KT-ID fisher test/7-7-fisher-galaxy_working.R |
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| diff -r aff861ca6e2b -r eb89ff215fb8 KT-ID fisher test/7-7-fisher-galaxy_working.R --- a/KT-ID fisher test/7-7-fisher-galaxy_working.R Mon Jan 14 15:40:43 2019 -0500 +++ b/KT-ID fisher test/7-7-fisher-galaxy_working.R Wed Feb 05 14:12:50 2020 -0500 |
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| @@ -666,33 +666,13 @@ NormalizationScore<-sum(numberofPY)/sum(numberofY) -#positions<-matrix(data = NA, nrow=20,ncol = 9) - -# write.xlsx(SDtable,file=SDtableAndPercentTable, sheetName = "Standard Deviation Table",col.names = FALSE,row.names = FALSE,append = TRUE) -# write.xlsx(PercentTable,file = SDtableAndPercentTable,sheetName = "Percent Table",col.names = FALSE,row.names = FALSE,append = TRUE) -# write.xlsx(SelectivitySheet,file = SDtableAndPercentTable,sheetName = "Site Selectivity",col.names = FALSE,row.names = FALSE,append = TRUE) -# write.xlsx(EPMtable,file=SDtableAndPercentTable,sheetName = "Endogenous Probability Matrix",col.names = FALSE,row.names = FALSE,append = TRUE) -# write.xlsx(NormalizationScore,file = SDtableAndPercentTable,sheetName = "Normalization Score",col.names = FALSE,row.names = FALSE,append = TRUE) NormalizationScore<-c("Normalization Score",NormalizationScore) -# write.table(x=c("SD Table"),file=SDtableAndPercentTable,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) -# write.table(SDtable,file=SDtableAndPercentTable,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) -# write.table(x=c("Percent Table"),file=SDtableAndPercentTable,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) -# write.table(PercentTable,file=SDtableAndPercentTable, append = TRUE,sep=",",row.names = FALSE, col.names = FALSE) - -# write.table(SelectivitySheet,file = SiteSelectivityTable_EndogenousProbabilityMatrix_NormalizationScore_CharacterizationTable, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE) -# write.table(x=c("Endogenous Probability Matrix"),file=SiteSelectivityTable_EndogenousProbabilityMatrix_NormalizationScore_CharacterizationTable,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE) -# write.table(EPMtable,file = SiteSelectivityTable_EndogenousProbabilityMatrix_NormalizationScore_CharacterizationTable, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE) write.table(NormalizationScore, file = SiteSelectivityTable_EndogenousProbabilityMatrix_NormalizationScore_CharacterizationTable, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE) ###################################### -#change this -WhichKinase<-"Btk" - -#change this -#Positionm6<-c("E") -6 -4 1 5 6 score from -7-7 and -4-4 and the little MCC table things bareSDs<-fisherupdown[1:20,2:16] bareSDs[20,8]<-3 @@ -824,44 +804,6 @@ 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(1:9) -# for (i in 1:15){ -# ExpectedValue<-0 -# for (j in 1:20){ -# value<-0 -# if (bareSDs[j,i]>1){ -# value<-AllMeans[j] -# } -# ExpectedValue<-ExpectedValue+value -# } -# SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100 -# } -# -# SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs -# SuperRow<-SelectivityRow - - -#90% whatevernness -# TPninetyone<-length(PositiveWeirdScores[PositiveWeirdScores>=0.91]) -# Senseninetyone<-TPninetyone/nrow(positivesubstrates) -# -# TNninetyone<-length(NegativeWeirdScores[NegativeWeirdScores<91]) -# Specninetyone<-TNninetyone/100 #create the MCC table |