comparison kinatestid_r/Kinatest-R.R @ 18:e16ca3e9fc49 draft

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17:26ef4add9f7b

SubstrateBackgroundFrequency<-SubstrateBackgroundFrequency[2:nrow(SubstrateBackgroundFrequency),]
Sub<-na.omit(SubstrateBackgroundFrequency)
SubstrateBackgroundFrequency<-Sub

args = commandArgs(trailingOnly=TRUE)
TodaysKinase<-args[1]

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

18:e16ca3e9fc49

SubstrateBackgroundFrequency<-SubstrateBackgroundFrequency[2:nrow(SubstrateBackgroundFrequency),]
Sub<-na.omit(SubstrateBackgroundFrequency)
SubstrateBackgroundFrequency<-Sub

args = commandArgs(trailingOnly=TRUE)
TodaysKinase<-as.character(args[1])

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(1:9)

for (i in 1:9){
  SumOfSigmasValue<-0
  for (j in 1:20){
    value<-0
    if (SDtable[j,i]>2){
      q=j+1
      value<-sum(substrates[,i]==SetOfAAs[q])
    }
    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(1:9)
for (i in 1:9){
  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

SelectivityRow<-rep(0,times=9)

for (q in 1:9) {
  SelectivityRow[q]<-(SumOfSigmaAAs[q]/SumOfExpectedSigmaAAs[q])*(SumOfSigmaAAs[q]/AAsAtPositions[q])
}

SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow)

SetOfAAs<-matrix(data = SetOfAAs,ncol = 1)

SDtableu<-SDtable