Mercurial > repos > jfb > kinatest_r_7_7testing

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

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author jfb
date Tue, 17 Apr 2018 13:07:41 -0400
parents 26ef4add9f7b
children 9e520c365624
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17:26ef4add9f7b 18:e16ca3e9fc49
17 SubstrateBackgroundFrequency<-SubstrateBackgroundFrequency[2:nrow(SubstrateBackgroundFrequency),] 17 SubstrateBackgroundFrequency<-SubstrateBackgroundFrequency[2:nrow(SubstrateBackgroundFrequency),]
18 Sub<-na.omit(SubstrateBackgroundFrequency) 18 Sub<-na.omit(SubstrateBackgroundFrequency)
19 SubstrateBackgroundFrequency<-Sub 19 SubstrateBackgroundFrequency<-Sub
20 20
21 args = commandArgs(trailingOnly=TRUE) 21 args = commandArgs(trailingOnly=TRUE)
22 TodaysKinase<-args[1] 22 TodaysKinase<-as.character(args[1])
23 23
24 24
25 25
26 26
27 27
526 526
527 527
528 SetOfAAs<-c("Letter","A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y") 528 SetOfAAs<-c("Letter","A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")
529 529
530 530
531 SumOfSigmaAAs<-c(1:15) 531 SumOfSigmaAAs<-c(1:9)
532 532
533 for (i in 1:15){ 533 for (i in 1:9){
534 SumOfSigmasValue<-0 534 SumOfSigmasValue<-0
535 for (j in 1:20){ 535 for (j in 1:20){
536 value<-0 536 value<-0
537 if (SDtable[j,i]>2){ 537 if (SDtable[j,i]>2){
538 value<-sum(substrates[,i]==SetOfAAs[j]) 538 q=j+1
539 value<-sum(substrates[,i]==SetOfAAs[q])
539 } 540 }
540 SumOfSigmasValue<-SumOfSigmasValue+value 541 SumOfSigmasValue<-SumOfSigmasValue+value
541 } 542 }
542 SumOfSigmaAAs[i]<-SumOfSigmasValue 543 SumOfSigmaAAs[i]<-SumOfSigmasValue
543 } 544 }
544 545
545 # AAs1<-length(substrates[,1])-sum(substrates[,1]=="") 546 AAs1<-length(substrates[,1])-sum(substrates[,1]=="")
546 # AAs2<-length(substrates[,2])-sum(substrates[,2]=="") 547 AAs2<-length(substrates[,2])-sum(substrates[,2]=="")
547 # AAs3<-length(substrates[,3])-sum(substrates[,3]=="") 548 AAs3<-length(substrates[,3])-sum(substrates[,3]=="")
548 # AAs4<-length(substrates[,4])-sum(substrates[,4]=="") 549 AAs4<-length(substrates[,4])-sum(substrates[,4]=="")
549 # AAs5<-length(substrates[,5])-sum(substrates[,5]=="") 550 AAs5<-length(substrates[,5])-sum(substrates[,5]=="")
550 # AAs6<-length(substrates[,6])-sum(substrates[,6]=="") 551 AAs6<-length(substrates[,6])-sum(substrates[,6]=="")
551 # AAs7<-length(substrates[,7])-sum(substrates[,7]=="") 552 AAs7<-length(substrates[,7])-sum(substrates[,7]=="")
552 # AAs8<-length(substrates[,8])-sum(substrates[,8]=="") 553 AAs8<-length(substrates[,8])-sum(substrates[,8]=="")
553 # AAs9<-length(substrates[,9])-sum(substrates[,9]=="") 554 AAs9<-length(substrates[,9])-sum(substrates[,9]=="")
554 # 555 AAsAtPositions<-c(AAs1,AAs2,AAs3,AAs4,AAs5,AAs6,AAs7,AAs8,AAs9)
555 #
556 #
557 # #AAsAtPositions<-c(AAs1,AAs2,AAs3,AAs4,AAs5,AAs6,AAs7,AAs8,AAs9)
558 # AAsAtPositions<-c(length(substrates[,1]),length(substrates[,2]),length(substrates[,3]),length(substrates[,4]), 556 # AAsAtPositions<-c(length(substrates[,1]),length(substrates[,2]),length(substrates[,3]),length(substrates[,4]),
559 # length(substrates[,5]),length(substrates[,6]),length(substrates[,7]),length(substrates[,8]), 557 # length(substrates[,5]),length(substrates[,6]),length(substrates[,7]),length(substrates[,8]),
560 # length(substrates[,9])) 558 # length(substrates[,9]))
561 559
562 SumOfExpectedSigmaAAs<-c(1:15) 560 SumOfExpectedSigmaAAs<-c(1:9)
563 for (i in 1:15){ 561 for (i in 1:9){
564 ExpectedValue<-0 562 ExpectedValue<-0
565 for (j in 1:20){ 563 for (j in 1:20){
566 value<-0 564 value<-0
567 if (SDtable[j,i]>2){ 565 if (SDtable[j,i]>2){
568 value<-AllMeans[j] 566 value<-AllMeans[j]
569 } 567 }
570 ExpectedValue<-ExpectedValue+value 568 ExpectedValue<-ExpectedValue+value
571 } 569 }
572 SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100 570 SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100
573 } 571 }
574 572
575 SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs 573 #SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs
574
575 SelectivityRow<-rep(0,times=9)
576
577 for (q in 1:9) {
578 SelectivityRow[q]<-(SumOfSigmaAAs[q]/SumOfExpectedSigmaAAs[q])*(SumOfSigmaAAs[q]/AAsAtPositions[q])
579 }
580
576 SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow) 581 SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow)
577 582
578 SetOfAAs<-matrix(data = SetOfAAs,ncol = 1) 583 SetOfAAs<-matrix(data = SetOfAAs,ncol = 1)
579 584
580 SDtableu<-SDtable 585 SDtableu<-SDtable