diff scoring function/.Rhistory @ 0:ed9068208721 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scoring function/.Rhistory	Fri Apr 26 16:36:21 2019 -0400
@@ -0,0 +1,284 @@
+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,""))