Mercurial > repos > jfb > kinatest_r_7_7testing

comparison kinatestid_r/Kinatest-R.R @ 19:9e520c365624 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jfb
date Tue, 17 Apr 2018 17:03:39 -0400
parents e16ca3e9fc49
children f7a6a3ec7710
comparison
equal deleted inserted replaced
18:e16ca3e9fc49 19:9e520c365624
525 } 525 }
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 SumOfSigmaAAs<-c(1:15)
531 SumOfSigmaAAs<-c(1:9) 531
532 532 for (i in 1:15){
533 for (i in 1:9){
534 SumOfSigmasValue<-0 533 SumOfSigmasValue<-0
535 for (j in 1:20){ 534 for (j in 1:20){
536 value<-0 535 value<-0
537 if (SDtable[j,i]>2){ 536 if (SDtable[j,i]>2){
538 q=j+1 537 q=j+1
555 AAsAtPositions<-c(AAs1,AAs2,AAs3,AAs4,AAs5,AAs6,AAs7,AAs8,AAs9) 554 AAsAtPositions<-c(AAs1,AAs2,AAs3,AAs4,AAs5,AAs6,AAs7,AAs8,AAs9)
556 # AAsAtPositions<-c(length(substrates[,1]),length(substrates[,2]),length(substrates[,3]),length(substrates[,4]), 555 # AAsAtPositions<-c(length(substrates[,1]),length(substrates[,2]),length(substrates[,3]),length(substrates[,4]),
557 # length(substrates[,5]),length(substrates[,6]),length(substrates[,7]),length(substrates[,8]), 556 # length(substrates[,5]),length(substrates[,6]),length(substrates[,7]),length(substrates[,8]),
558 # length(substrates[,9])) 557 # length(substrates[,9]))
559 558
560 SumOfExpectedSigmaAAs<-c(1:9) 559 SumOfExpectedSigmaAAs<-c(1:15)
561 for (i in 1:9){ 560 for (i in 1:15){
562 ExpectedValue<-0 561 ExpectedValue<-0
563 for (j in 1:20){ 562 for (j in 1:20){
564 value<-0 563 value<-0
565 if (SDtable[j,i]>2){ 564 if (SDtable[j,i]>2){
566 value<-AllMeans[j] 565 value<-AllMeans[j]
570 SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100 569 SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100
571 } 570 }
572 571
573 #SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs 572 #SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs
574 573
575 SelectivityRow<-rep(0,times=9) 574 SelectivityRow<-rep(0,times=15)
576 575
577 for (q in 1:9) { 576 for (q in 1:15) {
578 SelectivityRow[q]<-(SumOfSigmaAAs[q]/SumOfExpectedSigmaAAs[q])*(SumOfSigmaAAs[q]/AAsAtPositions[q]) 577 SelectivityRow[q]<-(SumOfSigmaAAs[q]/SumOfExpectedSigmaAAs[q])*(SumOfSigmaAAs[q]/AAsAtPositions[q])
579 } 578 }
580 579
581 SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow) 580 SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow)
582 581
583 SetOfAAs<-matrix(data = SetOfAAs,ncol = 1) 582 SetOfAAs<-matrix(data = SetOfAAs,ncol = 1)
584
585 SDtableu<-SDtable 583 SDtableu<-SDtable
586 HeaderSD<-c(-7:7) 584 HeaderSD<-c(-7:7)
587 SDtable<-rbind(HeaderSD,SDtableu) 585 SDtable<-rbind(HeaderSD,SDtableu)
588 row.names(SDtable)<-NULL 586 row.names(SDtable)<-NULL
589 SDtable<-data.frame(SetOfAAs,SDtable) 587 SDtable<-data.frame(SetOfAAs,SDtable)