Mercurial > repos > jfb > kinatest_scoring_function
view scoring function/.Rhistory @ 12:3437c03bb21e draft
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author | jfb |
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date | Thu, 03 Oct 2019 11:00:05 -0400 |
parents | ed9068208721 |
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install.packages("xlsx") package("xlsx") require(xlsx) ?read.xlsx ?read.xlsx("C:\Users\parkerlab\Downloads\ppse.xlsx") ?read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx") figs<-read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx") figs<-read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx",sheetIndex = 1) setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin") setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates") source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Difference Finder/all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R', echo=TRUE) setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates") source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Difference Finder/all stuff/difference finder for 2 overlaps proper names 7-7_1-15-2019.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Difference Finder/all stuff/Difference finderMADE 7 TO 7 fastversion 2-14-2019.R', echo=TRUE) setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates") source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/difference_finder-beba4066121e/difference_finder-beba4066121e/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/difference_finder-beba4066121e/difference_finder-beba4066121e/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/difference_finder-beba4066121e/difference_finder-beba4066121e/all stuff/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) D835YFinalMatrix FTLwtmotifs DataFilename<-"stRequiredData.RData" load(DataFilename) setwd("F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/Kinatest Fishertest/KT-ID fisher test") load(DataFilename) setwd("F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/ST fishertest/KT-ID fisher test") load(DataFilename) setwd("C:/Users/parkerlab/Downloads/stuff") source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) #put the names of your input files here FirstSubstrateSet<- read.csv("Galaxy1071-(17A_TiO2_Substrates.csv).csv", stringsAsFactors=FALSE) Firstsubbackfreq<- read.csv("Galaxy1072-(17A_TiO2_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE) SecondSubstrateSet<- read.csv("Galaxy1073-(17A_FeNTA_Substrates.csv) (1).csv", stringsAsFactors=FALSE) Secondsubbackfreq<- read.csv("Galaxy1074-(17A_FeNTA_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE) #I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon #the output files have both Y and xY, they shouldn't why is that happening? make it not happen #make sure that accession numbers stay locked to each motif, somehow #output should look just like the KALIP input #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps FullMotifsOnly_questionmark<-"NO" #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps TruncatedMotifsOnly_questionmark<-"NO" #if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps) Are_You_Looking_For_Commonality<-"NO" First_unshared_motifs_table<-"Substrates 3A no negatives.csv" First_unshared_subbackfreq<-"SBF 3A no negatives.csv" Second_unshared_motifs_table<-"Substrates 3B negatives.csv" Second_unshared_subbackfreq<-"SBF 3B negatives.csv" FirstCentralLetters<-FirstSubstrateSet[,11] SecondCentralLetters<-SecondSubstrateSet[,11] FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE) FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE) FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE) SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE) SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE) SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE) FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS") FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT") FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY") SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS") SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT") SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY") FirstCentralLetters->FirstSubstrateSet[,11] SecondCentralLetters->SecondSubstrateSet[,11] if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){ FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1) for (i in 1:nrow(FirstSubstrateSet)){ FTLwtletters<-FirstSubstrateSet[i,4:18] FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"] FTLwtletters<-paste(FTLwtletters, sep="", collapse="") leftspaces<-c() rightspaces<-c() YYYmotif <- unlist(strsplit(FTLwtletters, split = "")) YYYposition <- match(x = "x", table = YYYmotif) #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are #just 3 letters to the left of x YYYLettersToTheLeft <- YYYposition - 1 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the #variable the user puts in is if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) #add blank spaces if the motif has less than 4 letters to the left/right motif<-c(leftspaces,YYYmotif,rightspaces) #save that motif, which is the Y and +/- 4 amino acids, including truncation motif<-motif[!motif %in% "x"] motif<-paste(motif, sep="", collapse="") FTLwtletters<-motif FTLwtmotifs[i,1]<-FTLwtletters FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] } if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ motif<-YYYmotif #add blank spaces if the motif has less than 4 letters to the left/right motif<-c(leftspaces,YYYmotif,rightspaces) #save that motif, which is the Y and +/- 4 amino acids, including truncation motif<-motif[!motif %in% "x"] motif<-paste(motif, sep="", collapse="") FTLwtletters<-motif FTLwtmotifs[i,1]<-FTLwtletters FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] } } D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1) D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1) for (i in 1:nrow(SecondSubstrateSet)){ D835letters<-SecondSubstrateSet[i,4:18] D835letters<-D835letters[D835letters !="XXXXX"] D835letters<-paste(D835letters, sep="", collapse="") leftspaces<-c() rightspaces<-c() YYYmotif <- unlist(strsplit(D835letters, split = "")) YYYposition <- match(x = "x", table = YYYmotif) #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are #just 3 letters to the left of x YYYLettersToTheLeft <- YYYposition - 1 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the #variable the user puts in is if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) { leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft)) rightspaces<-rep(" ",times=7-(YYYLettersToTheRight)) #add blank spaces if the motif has less than 4 letters to the left/right motif<-c(leftspaces,YYYmotif,rightspaces) #save that motif, which is the Y and +/- 4 amino acids, including truncation motif<-motif[!motif %in% "x"] motif<-paste(motif, sep="", collapse="") D835letters<-motif D835Ymotifs[i,1]<-D835letters D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] } if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){ motif<-YYYmotif #add blank spaces if the motif has less than 4 letters to the left/right motif<-c(leftspaces,YYYmotif,rightspaces) #save that motif, which is the Y and +/- 4 amino acids, including truncation motif<-motif[!motif %in% "x"] motif<-paste(motif, sep="", collapse="") D835letters<-motif D835Ymotifs[i,1]<-D835letters D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3] } } names(FTLwtmotifs)<-FTLwtAccessionNumbers names(D835Ymotifs)<-D835YAccessionNumbers } length(names(FTLwtmotifs)) length(names(D835Ymotifs)) FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs] FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)] D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs] D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)] length(names(D835Ymotifs)) length(names(D835YmotifsFINAL)) for (k in 1:length(FTLwtmotifsFINAL)) { AN<-00000 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is #destroyed immediately after use for (m in 1:ncol(Firstsubbackfreq)) { AN <- as.character(Firstsubbackfreq[1, m]) if (grepl(pattern = AN, x = names(FTLwtmotifsFINAL[k]), fixed = TRUE) == TRUE) { outputmatrix <- as.character(Firstsubbackfreq[, m]) outputmatrix <- matrix(outputmatrix, nrow = 1) #with that accession number, find a match in the subbackfreq file and save it here FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) } } } columnalheader<-c(rep(NA,36)) FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1) for (k in 1:length(FTLwtmotifsFINAL)) { AN<-00000 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is #destroyed immediately after use for (m in 1:ncol(Firstsubbackfreq)) { AN <- as.character(Firstsubbackfreq[1, m]) if (grepl(pattern = AN, x = names(FTLwtmotifsFINAL[k]), fixed = TRUE) == TRUE) { outputmatrix <- as.character(Firstsubbackfreq[, m]) outputmatrix <- matrix(outputmatrix, nrow = 1) #with that accession number, find a match in the subbackfreq file and save it here FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix) } } } FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),] FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),] columnalheader<-c(rep(NA,36)) D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1) for (k in 1:length(D835YmotifsFINAL)) { #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is #destroyed immediately after use for (m in 1:ncol(Secondsubbackfreq)) { AN <- as.character(Secondsubbackfreq[1, m]) if (grepl(pattern = AN, x = names(D835YmotifsFINAL[k]), fixed = TRUE) == TRUE) { outputmatrix <- as.character(Secondsubbackfreq[, m]) outputmatrix <- matrix(outputmatrix, nrow = 1) #with that accession number, find a match in the subbackfreq file and save it here D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix) } } } D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),] D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),] FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2) tail(FTLoutputmatrix) D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2) tail(D835Youtputmatrix) length(names(D835YmotifsFINAL)) tail(D835YmotifsFINAL) tail(D835Ymotifs) tail(FTLwtmotifs) names(tail(D835Ymotifs)) names((D835Ymotifs)) names(FTLwtmotifs) head(FirstSubstrateSet) head(SecondSubstrateSet) source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE) source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finder MADE 7 TO 7 4-18-2019.R', echo=TRUE) ThisKinSheet<-read.csv("Fisher-Table.csv" header=FALSE, stringsAsFactors=FALSE) CharTable<-read.csv("Fisher-Char.csv", header = FALSE,stringsAsFactors = FALSE) setwd("F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID") CharTable<-read.csv("Fisher-Char.csv", header = FALSE,stringsAsFactors = FALSE) ThisKinSheet<-read.csv("Fisher-Table.csv", header=FALSE, stringsAsFactors=FALSE) ThisKinTable<-ThisKinSheet[2:22,] View(ThisKinTable) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) CharTable<-read.csv("Fisher-Char.csv", header = FALSE,stringsAsFactors = FALSE) ThisKinSheet<-read.csv("Fisher-Table.csv", header=FALSE, stringsAsFactors=FALSE) NormalizationScore<-ThisKinSheet[2,1] NormalizationScore<-CharTable[2,1] source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) RanksPeptides<-with(PeptidesWithRanks, order(Scores,AllActive)) write.table(RanksPeptides,file = "output.csv",append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",") RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks[,5), PeptidesWithRanks[,3]])] RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks[,5], PeptidesWithRanks[,3])] source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) Scores = Scores*-1 source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) Scores<-ThisKinGeneratedScores Scores<-Scores*-1 order(scores) order(Scores) Scores[order(Scores)] source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) LynActive source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) source('F:/ParkerLab Dropbox/Dropbox (Parker Lab)/Parker Lab Shared Files/Dropbox (Parker Lab)/Parker Lab Shared Files/CURRENT LAB MEMBERS/John B/Parker Lab/GalaxyP tools/scoring function KTID/KinatestFisherScoring.R', echo=TRUE) args toupper(6) Positionm6<-"123kjhsdfk245 23ddddd" Positionm6<-toupper(M6) M6<-"123kjhsdfk245 23ddddd" Positionm6<-toupper(M6) Positionm6<-gsub("[^a-zA-Z]", "", Positionm6) Positionm6<-unlist(strsplit(Positionm6,""))