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4
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1 #Difference finder for only 2
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2
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3 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
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4 FullMotifsOnly_questionmark<-"NO"
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5 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
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6 TruncatedMotifsOnly_questionmark<-"NO"
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7
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8 FirstSubstrateSet<- read.csv("Substrates 1A TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE)
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9 Firstsubbackfreq<- read.csv("SBF 1A TiO2 and FeNTA no duplicates.csv", header=FALSE, stringsAsFactors=FALSE)
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10
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11 SecondSubstrateSet<- read.csv("Substrates 1B TiO2 and FeNTA no duplicates.csv", stringsAsFactors=FALSE)
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12 Secondsubbackfreq<- read.csv("SBF 1B TiO2 and FeNTA no duplicates.csv", header=FALSE, stringsAsFactors=FALSE)
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13
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14 First_unshared_motifs_table<-"Substrates 1A no duplicates no negatives.csv"
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15 First_unshared_subbackfreq<-"SBF 1A no duplicates no negatives.csv"
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16
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17 Second_unshared_motifs_table<-"Substrates 1B no duplicates no negatives.csv"
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18 Second_unshared_subbackfreq<-"SBF 1B no duplicates no negatives.csv"
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19
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20
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21 LeftOfYLetters<-7
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22 RightOfYLetters<-7
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23
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24 if (FullMotifsOnly_questionmark=="YES"){
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25 FirstMotifs=rep(NA,times=nrow(FirstSubstrateSet))
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26 FirstAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
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27 leftspaces<-c()
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28 rightspaces<-c()
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29 for (i in 1:nrow(FirstSubstrateSet)){
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30 FirstLetters<-FirstSubstrateSet[i,7:15]
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31 FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
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32 FirstLetters<-paste(FirstLetters, sep="", collapse="")
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33
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34
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35 YYYmotif <- unlist(strsplit(FirstLetters, split = ""))
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36 YYYposition <- match(x = "x", table = YYYmotif)
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37 #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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38 #just 3 letters to the left of x
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39
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40 YYYLettersToTheLeft <- YYYposition - 1
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41 #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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42 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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43 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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44 #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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45 #variable the user puts in is
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46
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47 if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) {
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48 motif<-YYYmotif
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49 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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50 motif<-motif[!motif %in% "x"]
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51 motif<-paste(motif, sep="", collapse="")
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52 FirstLetters<-motif
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53 FirstMotifs[i]<-FirstLetters
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54 FirstAccessionNumbers[i]<-FirstSubstrateSet[i,3]
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55 }
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56
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57 }
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58 # FirstMotifs <- FirstMotifs[!is.na(FirstMotifs)]
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59 # FirstMotifs<-matrix(FirstMotifs,ncol = 1)
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60 #
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61
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62 SecondMotifs=rep(NA,times=nrow(FirstSubstrateSet))
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63 SecondAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
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64
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65 for (i in 1:nrow(SecondSubstrateSet)){
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66 SecondLetters<-SecondSubstrateSet[i,7:15]
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67 SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
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68 SecondLetters<-paste(SecondLetters, sep="", collapse="")
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69
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70
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71 YYYmotif <- unlist(strsplit(SecondLetters, split = ""))
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72 YYYposition <- match(x = "x", table = YYYmotif)
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73 #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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74 #just 3 letters to the left of x
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75
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76 YYYLettersToTheLeft <- YYYposition - 1
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77 #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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78 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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79 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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80 #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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81 #variable the user puts in is
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82
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83 if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) {
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84 motif<-YYYmotif
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85 #add blank spaces if the motif has less than 4 letters to the left/right
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86 motif<-c(leftspaces,YYYmotif,rightspaces)
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87 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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88 motif<-motif[!motif %in% "x"]
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89 motif<-paste(motif, sep="", collapse="")
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90 SecondLetters<-motif
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91 SecondMotifs[i]<-SecondLetters
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92 SecondAccessionNumbers[i]<-SecondSubstrateSet[i,3]
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93 }
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94 }
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95 names(FirstMotifs)<-FirstAccessionNumbers
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96 names(SecondMotifs)<-SecondAccessionNumbers
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97
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98
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99 # ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
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100 # ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
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101 if(1==0){
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102 for (i in 1:nrow(ThirdSubstrateSet)){
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103 ITDletters<-ThirdSubstrateSet[i,7:15]
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104 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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105 ITDletters<-paste(ITDletters, sep="", collapse="")
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106 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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107 YYYposition <- match(x = "x", table = YYYmotif)
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108 #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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109 #just 3 letters to the left of x
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110
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111 YYYLettersToTheLeft <- YYYposition - 1
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112 #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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113 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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114 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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115 #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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116 #variable the user puts in is
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117
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118 if (YYYLettersToTheLeft > 3 && YYYLettersToTheRight > 3) {
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119 motif<-YYYmotif
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120 #add blank spaces if the motif has less than 4 letters to the left/right
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121 motif<-c(leftspaces,YYYmotif,rightspaces)
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122 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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123 motif<-motif[!motif %in% "x"]
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124 motif<-paste(motif, sep="", collapse="")
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125 ITDletters<-motif
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126 ITDmotifs[i]<-ITDletters
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127 ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
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128
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129 }
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130 }
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131 }
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132 #names(ITDmotifs)<-ITDAccessionNumbers
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133 names(SecondMotifs)<-SecondAccessionNumbers
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134 names(FirstMotifs)<-FirstAccessionNumbers
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135 }
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136
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137
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138 ##############################################3
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139 #Truncated only
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140 if (TruncatedMotifsOnly_questionmark=="YES"){
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141 FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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142 FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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143
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144 for (i in 1:nrow(FirstSubstrateSet)){
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145 FirstLetters<-FirstSubstrateSet[i,7:15]
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146 FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
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147 FirstLetters<-paste(FirstLetters, sep="", collapse="")
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148
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149
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150 YYYmotif <- unlist(strsplit(FirstLetters, split = ""))
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151 YYYposition <- match(x = "x", table = YYYmotif)
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152 #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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153 #just 3 letters to the left of x
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154
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155 YYYLettersToTheLeft <- YYYposition - 1
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156 #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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157 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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158 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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159 #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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160 #variable the user puts in is
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161
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162 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
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163 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
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164 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
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165 #add blank spaces if the motif has less than 4 letters to the left/right
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166 motif<-c(leftspaces,YYYmotif,rightspaces)
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167 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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168 motif<-motif[!motif %in% "x"]
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169 motif<-paste(motif, sep="", collapse="")
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170 FirstLetters<-motif
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171 FirstMotifs[i,1]<-FirstLetters
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172 FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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173 }
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174
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175 }
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176
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177 SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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178 SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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179 i=2
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180 for (i in 1:nrow(SecondSubstrateSet)){
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181 SecondLetters<-SecondSubstrateSet[i,7:15]
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182 SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
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183 SecondLetters<-paste(SecondLetters, sep="", collapse="")
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184
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185
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186 YYYmotif <- unlist(strsplit(SecondLetters, split = ""))
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187 YYYposition <- match(x = "x", table = YYYmotif)
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188 #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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189 #just 3 letters to the left of x
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190
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191 YYYLettersToTheLeft <- YYYposition - 1
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192 #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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193 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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194 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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195 #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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196 #variable the user puts in is
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197
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198 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
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199 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
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200 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
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201 #add blank spaces if the motif has less than 4 letters to the left/right
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202 motif<-c(leftspaces,YYYmotif,rightspaces)
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203 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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204 motif<-motif[!motif %in% "x"]
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205 motif<-paste(motif, sep="", collapse="")
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206 SecondLetters<-motif
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207 SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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208 SecondMotifs[i,1]<-SecondLetters
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209 }
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210 }
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211
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212 # ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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213 # ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
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214 if(1==0){
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215 for (i in 1:nrow(ThirdSubstrateSet)){
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216 ITDletters<-ThirdSubstrateSet[i,7:15]
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217 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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218 ITDletters<-paste(ITDletters, sep="", collapse="")
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219 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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220 YYYposition <- match(x = "x", table = YYYmotif)
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221 #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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222 #just 3 letters to the left of x
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223
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224 YYYLettersToTheLeft <- YYYposition - 1
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225 #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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226 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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227 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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228 #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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229 #variable the user puts in is
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230
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231 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
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232 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
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233 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
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234 #add blank spaces if the motif has less than 4 letters to the left/right
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235 motif<-c(leftspaces,YYYmotif,rightspaces)
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236 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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237 motif<-motif[!motif %in% "x"]
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238 motif<-paste(motif, sep="", collapse="")
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239 ITDletters<-motif
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240 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
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241 ITDmotifs[i,1]<-ITDletters
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242 }
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243 }
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244 }
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245 names(FirstMotifs)<-FirstAccessionNumbers
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246 names(SecondMotifs)<-SecondAccessionNumbers
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247 #names(ITDmotifs)<-ITDAccessionNumbers
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248 }
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249
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250 ###############################################
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251 #ALL motifs, full and truncated
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252
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253 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
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254 #print("!")}
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255 FirstMotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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256 FirstAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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257
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258 for (i in 1:nrow(FirstSubstrateSet)){
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259 FirstLetters<-FirstSubstrateSet[i,7:15]
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260 FirstLetters<-FirstLetters[FirstLetters !="XXXXX"]
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261 FirstLetters<-paste(FirstLetters, sep="", collapse="")
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262 leftspaces<-c()
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263 rightspaces<-c()
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264
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265 YYYmotif <- unlist(strsplit(FirstLetters, split = ""))
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266 YYYposition <- match(x = "x", table = YYYmotif)
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267 #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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268 #just 3 letters to the left of x
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269
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270 YYYLettersToTheLeft <- YYYposition - 1
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271 #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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272 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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273 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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274 #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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275 #variable the user puts in is
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276
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277
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278 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
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279 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
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280 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
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281 #add blank spaces if the motif has less than 4 letters to the left/right
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282 motif<-c(leftspaces,YYYmotif,rightspaces)
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283 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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284 motif<-motif[!motif %in% "x"]
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285 motif<-paste(motif, sep="", collapse="")
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286 FirstLetters<-motif
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287 FirstMotifs[i,1]<-FirstLetters
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288 FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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289 }
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290
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291 if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
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292 motif<-YYYmotif
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293 #add blank spaces if the motif has less than 4 letters to the left/right
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294 motif<-c(leftspaces,YYYmotif,rightspaces)
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295 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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296 motif<-motif[!motif %in% "x"]
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297 motif<-paste(motif, sep="", collapse="")
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298 FirstLetters<-motif
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299 FirstMotifs[i,1]<-FirstLetters
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300 FirstAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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301
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302
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303 }
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304
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305 }
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306
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307 SecondMotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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308 SecondAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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309
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310 for (i in 1:nrow(SecondSubstrateSet)){
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311 SecondLetters<-SecondSubstrateSet[i,7:15]
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312 SecondLetters<-SecondLetters[SecondLetters !="XXXXX"]
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313 SecondLetters<-paste(SecondLetters, sep="", collapse="")
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314 leftspaces<-c()
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315 rightspaces<-c()
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316
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317 YYYmotif <- unlist(strsplit(SecondLetters, split = ""))
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318 YYYposition <- match(x = "x", table = YYYmotif)
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319 #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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320 #just 3 letters to the left of x
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321
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322 YYYLettersToTheLeft <- YYYposition - 1
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323 #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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324 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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325 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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326 #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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327 #variable the user puts in is
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328 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
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329 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
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330 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
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331 #add blank spaces if the motif has less than 4 letters to the left/right
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332 motif<-c(leftspaces,YYYmotif,rightspaces)
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333 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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334 motif<-motif[!motif %in% "x"]
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335 motif<-paste(motif, sep="", collapse="")
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336 SecondLetters<-motif
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337 SecondMotifs[i,1]<-SecondLetters
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338 SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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339 }
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340
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341 if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
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342 motif<-YYYmotif
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343 #add blank spaces if the motif has less than 4 letters to the left/right
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344 motif<-c(leftspaces,YYYmotif,rightspaces)
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345 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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346 motif<-motif[!motif %in% "x"]
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347 motif<-paste(motif, sep="", collapse="")
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348 SecondLetters<-motif
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349 SecondMotifs[i,1]<-SecondLetters
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350 SecondAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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351 }
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352 }
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353
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354
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355 #ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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356 #ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
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357 if(1==0){
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358 for (i in 1:nrow(ThirdSubstrateSet)){
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359 ITDletters<-ThirdSubstrateSet[i,7:15]
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360 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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361 ITDletters<-paste(ITDletters, sep="", collapse="")
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362 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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363 leftspaces<-c()
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364 rightspaces<-c()
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365 YYYposition <- match(x = "x", table = YYYmotif)
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366 #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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367 #just 3 letters to the left of x
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368
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369 YYYLettersToTheLeft <- YYYposition - 1
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370 #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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371 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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372 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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373 #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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374 #variable the user puts in is
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375 if (YYYLettersToTheLeft < 4 | YYYLettersToTheRight < 4) {
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376 leftspaces<-rep(" ",times=(4-YYYLettersToTheLeft))
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377 rightspaces<-rep(" ",times=4-(YYYLettersToTheRight))
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378 #add blank spaces if the motif has less than 4 letters to the left/right
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379 motif<-c(leftspaces,YYYmotif,rightspaces)
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380 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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381 motif<-motif[!motif %in% "x"]
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382 motif<-paste(motif, sep="", collapse="")
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383 ITDletters<-motif
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384 ITDmotifs[i,1]<-ITDletters
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385 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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386 }
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387
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388 if(YYYLettersToTheLeft>3 && YYYLettersToTheRight>3){
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389 motif<-YYYmotif
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390 #add blank spaces if the motif has less than 4 letters to the left/right
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391 motif<-c(leftspaces,YYYmotif,rightspaces)
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392 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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393 motif<-motif[!motif %in% "x"]
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394 motif<-paste(motif, sep="", collapse="")
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395 ITDletters<-motif
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396 ITDmotifs[i,1]<-ITDletters
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397 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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398 }
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399 }
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400 }
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401 names(FirstMotifs)<-FirstAccessionNumbers
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402 names(SecondMotifs)<-SecondAccessionNumbers
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403 #names(ITDmotifs)<-ITDAccessionNumbers
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404 }
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405
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406
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407 FirstMotifsFINAL<-FirstMotifs[!FirstMotifs %in% SecondMotifs]
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408 #FirstMotifsFINAL<-FirstMotifsFINAL[!FirstMotifsFINAL %in% ITDmotifs]
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409 FirstMotifsFINAL<-FirstMotifsFINAL[!duplicated(FirstMotifsFINAL)]
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410
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411
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412 # ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% SecondMotifs]
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413 # ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FirstMotifs]
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414 # ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
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415
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416
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417 SecondMotifsFINAL<-SecondMotifs[!SecondMotifs %in% FirstMotifs]
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418 #SecondMotifsFINAL<-SecondMotifsFINAL[!SecondMotifsFINAL %in% ITDmotifs]
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419 SecondMotifsFINAL<-SecondMotifsFINAL[!duplicated(SecondMotifsFINAL)]
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420
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421
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422 columnalheader<-c(rep(NA,36))
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423 FirstFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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424
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425 for (k in 1:length(FirstMotifsFINAL)) {
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426 AN<-00000
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427 #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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428 #destroyed immediately after use
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429 for (m in 2:ncol(Firstsubbackfreq)) {
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430 AN <- as.character(Firstsubbackfreq[2, m])
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431 #print(AN)}
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432 if (grepl(pattern = AN,
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433 x = names(FirstMotifsFINAL[k]),
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434 fixed = TRUE) == TRUE) {
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435 outputmatrix <- as.character(Firstsubbackfreq[, m])
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436 outputmatrix <- matrix(outputmatrix, nrow = 1)
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437 #with that accession number, find a match in the subbackfreq file and save it here
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438 FirstFinalMatrix<-rbind(FirstFinalMatrix,outputmatrix)
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439 # print(AN,outputmatrix)}
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440 }
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441 }
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442 }
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443 FirstFinalMatrix<-FirstFinalMatrix[!duplicated(FirstFinalMatrix),]
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444
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445 #columnalheader<-c(rep(NA,36))
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446 #ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
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447
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448 if(1==0){
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449 for (k in 1:length(ITDmotifsFINAL)) {
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450 AN<-00000
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451 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
452 #destroyed immediately after use
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453 for (m in 1:ncol(Thirdsubbackfreq)) {
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454 AN <- as.character(Thirdsubbackfreq[1, m])
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455 if (grepl(pattern = AN,
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456 x = names(ITDmotifsFINAL[k]),
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457 fixed = TRUE) == TRUE) {
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458 outputmatrix <- as.character(Thirdsubbackfreq[, m])
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459 outputmatrix <- matrix(outputmatrix, nrow = 1)
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460 #with that accession number, find a match in the subbackfreq file and save it here
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|
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461 ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
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462 }
|
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463 }
|
|
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464 }
|
|
|
465 ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),]
|
|
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466 }
|
|
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467
|
|
|
468 columnalheader<-c(rep(NA,36))
|
|
|
469 SecondFinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
470
|
|
|
471 for (k in 1:length(SecondMotifsFINAL)) {
|
|
|
472 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
473 #destroyed immediately after use
|
|
|
474 for (m in 1:ncol(Secondsubbackfreq)) {
|
|
|
475 AN <- as.character(Secondsubbackfreq[1, m])
|
|
|
476 if (grepl(pattern = AN,
|
|
|
477 x = names(SecondMotifsFINAL[k]),
|
|
|
478 fixed = TRUE) == TRUE) {
|
|
|
479 outputmatrix <- as.character(Secondsubbackfreq[, m])
|
|
|
480 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
481 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
482 SecondFinalMatrix<-rbind(SecondFinalMatrix,outputmatrix)
|
|
|
483 }
|
|
|
484 }
|
|
|
485 }
|
|
|
486 SecondFinalMatrix<-SecondFinalMatrix[!duplicated(SecondFinalMatrix),]
|
|
|
487 FTLoutputmatrix<-matrix(data=c(FirstMotifsFINAL,names(FirstMotifsFINAL)),ncol = 2)
|
|
|
488
|
|
|
489
|
|
|
490 write.table(x=FTLoutputmatrix,
|
|
|
491 file=First_unshared_motifs_table,
|
|
|
492 quote=FALSE, sep=",",
|
|
|
493 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
494
|
|
|
495 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
|
|
|
496 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
497 write.table(x=columnalheader,
|
|
|
498 file=First_unshared_subbackfreq,
|
|
|
499 quote=FALSE, sep=",",
|
|
|
500 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
501 FirstFinalMatrix<-FirstFinalMatrix[2:nrow(FirstFinalMatrix),]
|
|
|
502 write.table(x=FirstFinalMatrix,
|
|
|
503 file=First_unshared_subbackfreq,
|
|
|
504 quote=FALSE, sep=",",
|
|
|
505 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
506
|
|
|
507 ############################################################################################################
|
|
|
508
|
|
|
509 D835Youtputmatrix<-matrix(data=c(SecondMotifsFINAL,names(SecondMotifsFINAL)),ncol = 2)
|
|
|
510
|
|
|
511 write.table(x=D835Youtputmatrix,
|
|
|
512 file=Second_unshared_motifs_table,
|
|
|
513 quote=FALSE, sep=",",
|
|
|
514 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
515
|
|
|
516 columnalheader<-c(as.character(Firstsubbackfreq[1:36,1]))
|
|
|
517 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
518 write.table(x=columnalheader,
|
|
|
519 file=Second_unshared_subbackfreq,
|
|
|
520 quote=FALSE, sep=",",
|
|
|
521 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
522 SecondFinalMatrix<-SecondFinalMatrix[2:nrow(SecondFinalMatrix),]
|
|
|
523 write.table(x=SecondFinalMatrix,
|
|
|
524 file=Second_unshared_subbackfreq,
|
|
|
525 quote=FALSE, sep=",",
|
|
|
526 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
527
|
|
|
528 ############################################################################################################
|
|
|
529
|
|
|
530 # ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2)
|
|
|
531 #
|
|
|
532 # write.table(x=ITDoutputmatrix,
|
|
|
533 # file=Third_unshared_motifs_table,
|
|
|
534 # quote=FALSE, sep=",",
|
|
|
535 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
536 #
|
|
|
537 # columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
538 # columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
539 # write.table(x=columnalheader,
|
|
|
540 # file=Third_unshared_subbackfreq,
|
|
|
541 # quote=FALSE, sep=",",
|
|
|
542 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
543 # ITDFinalMatrix<-ITDFinalMatrix[2:nrow(ITDFinalMatrix),]
|
|
|
544 # write.table(x=ITDFinalMatrix,
|
|
|
545 # file=Third_unshared_subbackfreq,
|
|
|
546 # quote=FALSE, sep=",",
|
|
|
547 # row.names=FALSE,col.names = FALSE, na="", append=TRUE) |
