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1 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE,colClasses = "character")
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2 Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)
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3 SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE,colClasses = "character")
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4 Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE)
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5 #this brings in the input files
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6
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7
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8 First_unshared_motifs_table<-"1RS.csv"
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9 First_unshared_subbackfreq<-"1RSBF.csv"
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10 Second_unshared_motifs_table<-"2RS.csv"
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11 Second_unshared_subbackfreq<-"2RSBF.csv"
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12 #this names the output files
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13
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14 EmptySubHeader<-colnames(FirstSubstrateSet)
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15 EmptySubHeader<-matrix(EmptySubHeader, nrow=1)
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16 EmptySBFHeader<-Firstsubbackfreq[,1]
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17 #this creates the headers which comes from the input files, so that the output files can be given this header so that they will look identical to the input files
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18
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19
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20 #the below code is used to ensure that all phospho-amino acids get marked with an "x" to denote their phosphoness
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21 FirstCentralLetters<-FirstSubstrateSet[,11]
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22 SecondCentralLetters<-SecondSubstrateSet[,11]
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23 #the phospho AAs are always found in position 12, so take them from there
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24
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25 FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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26 FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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27 FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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28 #use an 3 apply functions to create vectors, these vetors have true values where they find an S, T or Y.
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29 #so FirstEsses has a True anywhere it sees an S, and FirstTees has a True anywhere it sees a Y
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30
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31 SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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32 SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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33 SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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34 #do the same for the second substrate set's central letters
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35
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36 FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
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37 FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
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38 FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")
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39 #where there is a True value in FirstEsses, replace that value in the original substrate set with an xS. This is because there was originally an S in that
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40 #position, and I want that S to be marked with an x, denoting phospho
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41
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42 SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
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43 SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
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44 SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")
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45
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46 FirstCentralLetters->FirstSubstrateSet[,11]
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47 SecondCentralLetters->SecondSubstrateSet[,11]
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48 #then I put these x-marked letters back where I found them, in position 11 of the substrate sets
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49
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50 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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51 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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52
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53 for (i in 1:nrow(FirstSubstrateSet)){
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54 FTLwtletters<-FirstSubstrateSet[i,4:18]
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55 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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56 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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57 leftspaces<-c()
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58 rightspaces<-c()
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59
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60 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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61 YYYposition <- match(x = "x", table = YYYmotif)
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62 #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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63 #just 3 letters to the left of x
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64
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65 YYYLettersToTheLeft <- YYYposition - 1
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66 #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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67 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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68 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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69 #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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70 #variable the user puts in is
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71
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72
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73 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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74 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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75 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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76 #add blank spaces if the motif has less than 4 letters to the left/right
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77 motif<-c(leftspaces,YYYmotif,rightspaces)
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78 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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79 motif<-motif[!motif %in% "x"]
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80 motif<-paste(motif, sep="", collapse="")
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81 FTLwtletters<-motif
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82 FTLwtmotifs[i,1]<-FTLwtletters
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83 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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84 }
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85
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86 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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87 motif<-YYYmotif
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88 #add blank spaces if the motif has less than 4 letters to the left/right
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89 motif<-c(leftspaces,YYYmotif,rightspaces)
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90 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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91 motif<-motif[!motif %in% "x"]
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92 motif<-paste(motif, sep="", collapse="")
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93 FTLwtletters<-motif
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94 FTLwtmotifs[i,1]<-FTLwtletters
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95 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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96
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97
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98 }
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99
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100 }
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101
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102 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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103 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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104
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105 for (i in 1:nrow(SecondSubstrateSet)){
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106 D835letters<-SecondSubstrateSet[i,4:18]
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107 D835letters<-D835letters[D835letters !="XXXXX"]
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108 D835letters<-paste(D835letters, sep="", collapse="")
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109 leftspaces<-c()
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110 rightspaces<-c()
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111
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112 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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113 YYYposition <- match(x = "x", table = YYYmotif)
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114 #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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115 #just 3 letters to the left of x
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116
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117 YYYLettersToTheLeft <- YYYposition - 1
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118 #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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119 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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120 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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121 #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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122 #variable the user puts in is
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123 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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124 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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125 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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126 #add blank spaces if the motif has less than 4 letters to the left/right
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127 motif<-c(leftspaces,YYYmotif,rightspaces)
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128 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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129 motif<-motif[!motif %in% "x"]
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130 motif<-paste(motif, sep="", collapse="")
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131 D835letters<-motif
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132 D835Ymotifs[i,1]<-D835letters
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133 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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134 }
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135
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136 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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137 motif<-YYYmotif
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138 #add blank spaces if the motif has less than 4 letters to the left/right
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139 motif<-c(leftspaces,YYYmotif,rightspaces)
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140 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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141 motif<-motif[!motif %in% "x"]
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142 motif<-paste(motif, sep="", collapse="")
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143 D835letters<-motif
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144 D835Ymotifs[i,1]<-D835letters
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145 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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146 }
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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
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153 FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
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154 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
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155
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156 D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
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157 D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
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158
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159
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160 columnalheader<-c(rep(NA,36))
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161 FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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162
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163 FLTheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
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164
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165 if (length(FTLwtmotifsFINAL)>0){
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166 for (k in 1:length(FTLwtmotifsFINAL)) {
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167 AN<-00000
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168 #it is necessary to destroy the accession number multiple times to ensure it is
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169 #destroyed immediately after use
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170 for (m in 1:ncol(Firstsubbackfreq)) {
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171 AN <- as.character(Firstsubbackfreq[1, m])
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172 if (grepl(pattern = AN,
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173 x = names(FTLwtmotifsFINAL[k]),
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174 fixed = TRUE) == TRUE) {
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175 outputmatrix <- as.character(Firstsubbackfreq[, m])
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176 outputmatrix <- matrix(outputmatrix, nrow = 1)
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177 #with that accession number, find a match in the subbackfreq file and save it here
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178 FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
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179 }
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180 }
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181 }
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182 FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
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183 FTLFinalMatrix<-FTLFinalMatrix[2:nrow(FTLFinalMatrix),]
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184
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185
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186 FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
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187 # FLTheader<-unlist(FLTheader)
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188 lefthandFLT<-matrix(data = rep(NA,times=2*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
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189 righthandFLT<-matrix(data = rep(NA,times=1*nrow(FTLoutputmatrix)),nrow=nrow(FTLoutputmatrix))
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190 FLTaccessionset<-FTLoutputmatrix[,2]
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191 FTLmeat<-sapply(FTLoutputmatrix[,1], strsplit, "")
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192 FTLmeat<-sapply(FTLmeat, unlist)
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193 colnames(FTLmeat)<-NULL
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194 FTLmeat<-t(FTLmeat)
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195
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196 FTLoutputmatrix2<-cbind(lefthandFLT,FLTaccessionset,FTLmeat,righthandFLT)
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197 colnames(FTLoutputmatrix2)<-NULL
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198 rownames(FTLoutputmatrix2)<-NULL
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199 colnames(FLTheader)<-NULL
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200 rownames(FLTheader)<-NULL
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201
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202
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203 FirstCentralLettersAGAIN<-FTLoutputmatrix2[,11]
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204
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205 FirstEsses<-sapply(FirstCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
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206 FirstTees<-sapply(FirstCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
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207 FirstWys<-sapply(FirstCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)
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208
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209 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstEsses,"xS")
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210 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstTees,"xT")
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211 FirstCentralLettersAGAIN<-replace(FirstCentralLettersAGAIN,FirstWys,"xY")
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212
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213 FirstCentralLettersAGAIN->FTLoutputmatrix2[,11]
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214
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215 FTLoutputmatrix2<-rbind(FLTheader,FTLoutputmatrix2)
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216
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217 write.table(x=FTLoutputmatrix2,
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218 file=First_unshared_motifs_table,
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219 quote=FALSE, sep=",",
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220 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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221
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222 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
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223 columnalheader<-matrix(columnalheader,nrow = 1)
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224 write.table(x=columnalheader,
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225 file=First_unshared_subbackfreq,
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226 quote=FALSE, sep=",",
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227 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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228
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229 write.table(x=FTLFinalMatrix,
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230 file=First_unshared_subbackfreq,
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231 quote=FALSE, sep=",",
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232 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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233 } else{
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234 FTLFinalMatrix<-columnalheader
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235 write.table(x=EmptySubHeader,
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236 file=First_unshared_motifs_table,
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237 quote=FALSE, sep=",",
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238 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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239
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240 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
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241 columnalheader<-matrix(columnalheader,nrow = 1)
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242 write.table(x=columnalheader,
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243 file=First_unshared_subbackfreq,
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244 quote=FALSE, sep=",",
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245 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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246 }
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247
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248
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249 columnalheader<-c(rep(NA,36))
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250 D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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251
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252 if (length(D835YmotifsFINAL)>0){
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253 for (k in 1:length(D835YmotifsFINAL)) {
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254 #it is necessary to destroy the accession number multiple times to ensure it is
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255 #destroyed immediately after use
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256 for (m in 1:ncol(Secondsubbackfreq)) {
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257 AN <- as.character(Secondsubbackfreq[1, m])
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258 if (grepl(pattern = AN,
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259 x = names(D835YmotifsFINAL[k]),
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260 fixed = TRUE) == TRUE) {
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261 outputmatrix <- as.character(Secondsubbackfreq[, m])
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262 outputmatrix <- matrix(outputmatrix, nrow = 1)
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263 #with that accession number, find a match in the subbackfreq file and save it here
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264 D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
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265 }
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266 }
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267 }
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268 D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
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269 D835YFinalMatrix<-D835YFinalMatrix[2:nrow(D835YFinalMatrix),]
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270
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271 D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
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272
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273 D835Yheader<-c("Substrate","Species","Reference","-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7","Phosphite")
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274 # D835Yheader<-unlist(D835Yheader)
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275 lefthandD835<-matrix(data = rep(NA,times=2*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
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276 righthandD835<-matrix(data = rep(NA,times=1*nrow(D835Youtputmatrix)),nrow=nrow(D835Youtputmatrix))
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277 D835Yaset<-D835Youtputmatrix[,2]
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278 D835meat<-sapply(D835Youtputmatrix[,1], strsplit, "")
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279 D835meat<-sapply(D835meat, unlist)
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280 colnames(D835meat)<-NULL
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281 D835meat<-t(D835meat)
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282
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283 D835Youtputmatrix2<-cbind(lefthandD835,D835Yaset,D835meat,righthandD835)
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284 colnames(D835Youtputmatrix2)<-NULL
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285 rownames(D835Youtputmatrix2)<-NULL
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286 colnames(D835Yheader)<-NULL
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287 rownames(D835Yheader)<-NULL
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288
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289
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290 SecondCentralLettersAGAIN<-D835Youtputmatrix2[,11]
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291
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292 SecondEsses<-sapply(SecondCentralLettersAGAIN, grepl, pattern="S", ignore.case=TRUE)
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293 SecondTees<-sapply(SecondCentralLettersAGAIN, grepl, pattern="T", ignore.case=TRUE)
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294 SecondWys<-sapply(SecondCentralLettersAGAIN, grepl, pattern="Y", ignore.case=TRUE)
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295
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296 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondEsses,"xS")
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297 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondTees,"xT")
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298 SecondCentralLettersAGAIN<-replace(SecondCentralLettersAGAIN,SecondWys,"xY")
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299
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300 SecondCentralLettersAGAIN->D835Youtputmatrix2[,11]
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301
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302 D835Youtputmatrix2<-rbind(D835Yheader,D835Youtputmatrix2)
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303
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304 write.table(x=D835Youtputmatrix2,
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305 file=Second_unshared_motifs_table,
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306 quote=FALSE, sep=",",
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307 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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308
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309 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
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310 columnalheader<-matrix(columnalheader,nrow = 1)
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311 write.table(x=columnalheader,
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312 file=Second_unshared_subbackfreq,
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313 quote=FALSE, sep=",",
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314 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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315
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316 write.table(x=D835YFinalMatrix,
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317 file=Second_unshared_subbackfreq,
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318 quote=FALSE, sep=",",
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319 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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320 } else {
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321 D835YFinalMatrix<- columnalheader
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322 write.table(x=EmptySubHeader,
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323 file=Second_unshared_motifs_table,
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324 quote=FALSE, sep=",",
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325 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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326
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327 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
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328 columnalheader<-matrix(columnalheader,nrow = 1)
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329 write.table(x=columnalheader,
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330 file=Second_unshared_subbackfreq,
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331 quote=FALSE, sep=",",
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332 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
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333 } |