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1 install.packages("xlsx")
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2 package("xlsx")
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3 require(xlsx)
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4 ?read.xlsx
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5 ?read.xlsx("C:\Users\parkerlab\Downloads\ppse.xlsx")
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6 ?read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx")
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7 figs<-read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx")
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8 figs<-read.xlsx("C:/Users/parkerlab/Downloads/ppse.xlsx",sheetIndex = 1)
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9 setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin")
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10 setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates")
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11 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)
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12 setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates")
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13 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)
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14 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)
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15 setwd("C:/Users/parkerlab/Desktop/Laura Difference Finder files/LKB1 trypsin/No duplicates")
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16 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)
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17 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)
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18 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)
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19 D835YFinalMatrix
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20 FTLwtmotifs
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21 DataFilename<-"stRequiredData.RData"
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22 load(DataFilename)
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23 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")
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24 load(DataFilename)
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25 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")
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26 load(DataFilename)
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27 setwd("C:/Users/parkerlab/Downloads/stuff")
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28 source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE)
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29 #put the names of your input files here
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30 FirstSubstrateSet<- read.csv("Galaxy1071-(17A_TiO2_Substrates.csv).csv", stringsAsFactors=FALSE)
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31 Firstsubbackfreq<- read.csv("Galaxy1072-(17A_TiO2_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE)
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32 SecondSubstrateSet<- read.csv("Galaxy1073-(17A_FeNTA_Substrates.csv) (1).csv", stringsAsFactors=FALSE)
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33 Secondsubbackfreq<- read.csv("Galaxy1074-(17A_FeNTA_SubstrateBackgroundFrequency.csv).csv", header=FALSE, stringsAsFactors=FALSE)
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34 #I should make an SOP for this. Problems we encountered: no x in the xY motif, and the kilodemon
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35 #the output files have both Y and xY, they shouldn't why is that happening? make it not happen
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36 #make sure that accession numbers stay locked to each motif, somehow
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37 #output should look just like the KALIP input
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38 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
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39 FullMotifsOnly_questionmark<-"NO"
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40 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
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41 TruncatedMotifsOnly_questionmark<-"NO"
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42 #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)
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43 Are_You_Looking_For_Commonality<-"NO"
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44 First_unshared_motifs_table<-"Substrates 3A no negatives.csv"
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45 First_unshared_subbackfreq<-"SBF 3A no negatives.csv"
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46 Second_unshared_motifs_table<-"Substrates 3B negatives.csv"
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47 Second_unshared_subbackfreq<-"SBF 3B negatives.csv"
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48 FirstCentralLetters<-FirstSubstrateSet[,11]
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49 SecondCentralLetters<-SecondSubstrateSet[,11]
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50 FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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51 FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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52 FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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53 SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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54 SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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55 SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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56 FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
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57 FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
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58 FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")
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59 SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
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60 SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
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61 SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")
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62 FirstCentralLetters->FirstSubstrateSet[,11]
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63 SecondCentralLetters->SecondSubstrateSet[,11]
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64 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
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65 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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66 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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67 for (i in 1:nrow(FirstSubstrateSet)){
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68 FTLwtletters<-FirstSubstrateSet[i,4:18]
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69 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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70 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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71 leftspaces<-c()
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72 rightspaces<-c()
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73 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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74 YYYposition <- match(x = "x", table = YYYmotif)
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75 #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
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76 #just 3 letters to the left of x
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77 YYYLettersToTheLeft <- YYYposition - 1
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78 #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
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79 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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80 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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81 #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
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82 #variable the user puts in is
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83 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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84 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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85 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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86 #add blank spaces if the motif has less than 4 letters to the left/right
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87 motif<-c(leftspaces,YYYmotif,rightspaces)
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88 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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89 motif<-motif[!motif %in% "x"]
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90 motif<-paste(motif, sep="", collapse="")
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91 FTLwtletters<-motif
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92 FTLwtmotifs[i,1]<-FTLwtletters
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93 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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94 }
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95 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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96 motif<-YYYmotif
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97 #add blank spaces if the motif has less than 4 letters to the left/right
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98 motif<-c(leftspaces,YYYmotif,rightspaces)
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99 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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100 motif<-motif[!motif %in% "x"]
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101 motif<-paste(motif, sep="", collapse="")
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102 FTLwtletters<-motif
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103 FTLwtmotifs[i,1]<-FTLwtletters
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104 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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105 }
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106 }
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107 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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108 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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109 for (i in 1:nrow(SecondSubstrateSet)){
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110 D835letters<-SecondSubstrateSet[i,4:18]
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111 D835letters<-D835letters[D835letters !="XXXXX"]
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112 D835letters<-paste(D835letters, sep="", collapse="")
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113 leftspaces<-c()
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114 rightspaces<-c()
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115 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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116 YYYposition <- match(x = "x", table = YYYmotif)
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117 #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
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118 #just 3 letters to the left of x
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119 YYYLettersToTheLeft <- YYYposition - 1
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120 #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
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121 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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122 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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123 #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
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124 #variable the user puts in is
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125 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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126 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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127 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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128 #add blank spaces if the motif has less than 4 letters to the left/right
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129 motif<-c(leftspaces,YYYmotif,rightspaces)
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130 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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131 motif<-motif[!motif %in% "x"]
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132 motif<-paste(motif, sep="", collapse="")
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133 D835letters<-motif
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134 D835Ymotifs[i,1]<-D835letters
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135 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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136 }
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137 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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138 motif<-YYYmotif
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139 #add blank spaces if the motif has less than 4 letters to the left/right
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140 motif<-c(leftspaces,YYYmotif,rightspaces)
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141 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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142 motif<-motif[!motif %in% "x"]
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143 motif<-paste(motif, sep="", collapse="")
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144 D835letters<-motif
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145 D835Ymotifs[i,1]<-D835letters
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146 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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147 }
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148 }
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149 names(FTLwtmotifs)<-FTLwtAccessionNumbers
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150 names(D835Ymotifs)<-D835YAccessionNumbers
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151 }
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152 length(names(FTLwtmotifs))
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153 length(names(D835Ymotifs))
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154 FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
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155 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
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156 D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
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157 D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
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158 length(names(D835Ymotifs))
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159 length(names(D835YmotifsFINAL))
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160 for (k in 1:length(FTLwtmotifsFINAL)) {
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161 AN<-00000
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162 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
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163 #destroyed immediately after use
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164 for (m in 1:ncol(Firstsubbackfreq)) {
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165 AN <- as.character(Firstsubbackfreq[1, m])
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166 if (grepl(pattern = AN,
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167 x = names(FTLwtmotifsFINAL[k]),
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168 fixed = TRUE) == TRUE) {
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169 outputmatrix <- as.character(Firstsubbackfreq[, m])
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170 outputmatrix <- matrix(outputmatrix, nrow = 1)
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171 #with that accession number, find a match in the subbackfreq file and save it here
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172 FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
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173 }
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174 }
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175 }
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176 columnalheader<-c(rep(NA,36))
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177 FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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178 for (k in 1:length(FTLwtmotifsFINAL)) {
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179 AN<-00000
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180 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
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181 #destroyed immediately after use
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182 for (m in 1:ncol(Firstsubbackfreq)) {
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183 AN <- as.character(Firstsubbackfreq[1, m])
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184 if (grepl(pattern = AN,
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185 x = names(FTLwtmotifsFINAL[k]),
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186 fixed = TRUE) == TRUE) {
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187 outputmatrix <- as.character(Firstsubbackfreq[, m])
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188 outputmatrix <- matrix(outputmatrix, nrow = 1)
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189 #with that accession number, find a match in the subbackfreq file and save it here
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190 FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
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191 }
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192 }
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193 }
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194 FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
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195 FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),]
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196 columnalheader<-c(rep(NA,36))
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197 D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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198 for (k in 1:length(D835YmotifsFINAL)) {
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199 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
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200 #destroyed immediately after use
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201 for (m in 1:ncol(Secondsubbackfreq)) {
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202 AN <- as.character(Secondsubbackfreq[1, m])
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203 if (grepl(pattern = AN,
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204 x = names(D835YmotifsFINAL[k]),
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205 fixed = TRUE) == TRUE) {
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206 outputmatrix <- as.character(Secondsubbackfreq[, m])
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207 outputmatrix <- matrix(outputmatrix, nrow = 1)
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208 #with that accession number, find a match in the subbackfreq file and save it here
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209 D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
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210 }
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211 }
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212 }
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213 D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
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214 D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),]
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215 FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
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216 tail(FTLoutputmatrix)
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217 D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
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218 source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE)
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219 D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
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220 tail(D835Youtputmatrix)
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221 length(names(D835YmotifsFINAL))
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222 tail(D835YmotifsFINAL)
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223 tail(D835Ymotifs)
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224 tail(FTLwtmotifs)
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225 names(tail(D835Ymotifs))
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226 names((D835Ymotifs))
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227 names(FTLwtmotifs)
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228 head(FirstSubstrateSet)
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229 head(SecondSubstrateSet)
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230 source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE)
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231 source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE)
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232 source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finderMADE 7 TO 7 1-15-2019.R', echo=TRUE)
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233 source('C:/Users/parkerlab/Desktop/Laura Difference Finder files/Difference finder MADE 7 TO 7 4-18-2019.R', echo=TRUE)
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234 ThisKinSheet<-read.csv("Fisher-Table.csv" header=FALSE, stringsAsFactors=FALSE)
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235 CharTable<-read.csv("Fisher-Char.csv", header = FALSE,stringsAsFactors = FALSE)
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236 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")
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237 CharTable<-read.csv("Fisher-Char.csv", header = FALSE,stringsAsFactors = FALSE)
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238 ThisKinSheet<-read.csv("Fisher-Table.csv", header=FALSE, stringsAsFactors=FALSE)
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239 ThisKinTable<-ThisKinSheet[2:22,]
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240 View(ThisKinTable)
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241 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)
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242 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)
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243 CharTable<-read.csv("Fisher-Char.csv", header = FALSE,stringsAsFactors = FALSE)
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244 ThisKinSheet<-read.csv("Fisher-Table.csv", header=FALSE, stringsAsFactors=FALSE)
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245 NormalizationScore<-ThisKinSheet[2,1]
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246 NormalizationScore<-CharTable[2,1]
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247 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)
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248 RanksPeptides<-with(PeptidesWithRanks, order(Scores,AllActive))
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249 write.table(RanksPeptides,file = "output.csv",append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",")
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250 RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks[,5), PeptidesWithRanks[,3]])]
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251 RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks[,5], PeptidesWithRanks[,3])]
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252 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)
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253 Scores = Scores*-1
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254 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)
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255 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)
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256 Scores<-ThisKinGeneratedScores
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257 Scores<-Scores*-1
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258 order(scores)
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259 order(Scores)
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260 Scores[order(Scores)]
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261 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)
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262 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)
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263 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)
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264 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)
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265 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)
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266 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)
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267 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)
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268 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)
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269 LynActive
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270 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)
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271 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)
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272 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)
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273 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)
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274 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)
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275 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)
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276 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)
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277 args
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278 toupper(6)
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279 Positionm6<-"123kjhsdfk245 23ddddd"
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280 Positionm6<-toupper(M6)
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281 M6<-"123kjhsdfk245 23ddddd"
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282 Positionm6<-toupper(M6)
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283 Positionm6<-gsub("[^a-zA-Z]", "", Positionm6)
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284 Positionm6<-unlist(strsplit(Positionm6,""))
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