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9
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1 ?rnorm
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2 ?rnorm
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3 ?rnorm
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4 pwr
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5 ?pwr
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6 ??pwr
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7 power.t.test(n=6, power = .7, type = "two.sample", alternative = "two.sided")
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8 power.t.test(n=6, power = .9, type = "two.sample", alternative = "two.sided")
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9 ?power.t.test
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10 power.t.test(n=5, sd=1000, power = .7, type = "paired", alternative = "one.sided")
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11 10^4
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12 power.t.test(n=5, sd=10000, power = .7, type = "paired", alternative = "one.sided")
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13 power.t.test(n=10, delta = 7, sd=10, type = "paired", alternative = "one.sided")
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14 setwd("C:/Users/John Blankenhor/Downloads/difference_finder-4dd15c41d9e7/difference_finder-4dd15c41d9e7/all stuff")
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15 #put the names of your input files here
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16 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
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17 Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)
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18 FirstSubstrateSet
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19 EmptySubHeader<-First_unshared_motifs_table[1,]
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20 First_unshared_motifs_table<-"1RS.csv"
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21 First_unshared_subbackfreq<-"1RSBF.csv"
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22 #put the names of your input files here
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23 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
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24 Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)
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25 EmptySubHeader<-FirstSubstrateSet[1,]
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26 head(Firstsubbackfreq)
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27 EmptySBFHeader<-Firstsubbackfreq[,1]
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28 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
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29 FullMotifsOnly_questionmark<-"NO"
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30 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
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31 TruncatedMotifsOnly_questionmark<-"NO"
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32 #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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33 Are_You_Looking_For_Commonality<-"NO"
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34 #put the names of your input files here
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35 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
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36 Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)
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37 SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE)
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38 Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE)
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39 First_unshared_motifs_table<-"1RS.csv"
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40 First_unshared_subbackfreq<-"1RSBF.csv"
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41 Second_unshared_motifs_table<-"2RS.csv"
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42 Second_unshared_subbackfreq<-"2RSBF.csv"
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43 EmptySubHeader<-FirstSubstrateSet[1,]
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44 EmptySBFHeader<-Firstsubbackfreq[,1]
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45 FirstCentralLetters<-FirstSubstrateSet[,11]
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46 SecondCentralLetters<-SecondSubstrateSet[,11]
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47 FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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48 FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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49 FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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50 SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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51 SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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52 SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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53 FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
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54 FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
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55 FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")
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56 SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
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57 SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
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58 SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")
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59 FirstCentralLetters->FirstSubstrateSet[,11]
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60 SecondCentralLetters->SecondSubstrateSet[,11]
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61 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
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62 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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63 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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64 for (i in 1:nrow(FirstSubstrateSet)){
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65 FTLwtletters<-FirstSubstrateSet[i,4:18]
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66 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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67 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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68 leftspaces<-c()
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69 rightspaces<-c()
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70 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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71 YYYposition <- match(x = "x", table = YYYmotif)
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72 #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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73 #just 3 letters to the left of x
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74 YYYLettersToTheLeft <- YYYposition - 1
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75 #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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76 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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77 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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78 #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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79 #variable the user puts in is
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80 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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81 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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82 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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83 #add blank spaces if the motif has less than 4 letters to the left/right
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84 motif<-c(leftspaces,YYYmotif,rightspaces)
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85 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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86 motif<-motif[!motif %in% "x"]
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87 motif<-paste(motif, sep="", collapse="")
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88 FTLwtletters<-motif
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89 FTLwtmotifs[i,1]<-FTLwtletters
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90 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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91 }
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92 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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93 motif<-YYYmotif
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94 #add blank spaces if the motif has less than 4 letters to the left/right
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95 motif<-c(leftspaces,YYYmotif,rightspaces)
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96 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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97 motif<-motif[!motif %in% "x"]
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98 motif<-paste(motif, sep="", collapse="")
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99 FTLwtletters<-motif
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100 FTLwtmotifs[i,1]<-FTLwtletters
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101 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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102 }
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103 }
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104 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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105 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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106 for (i in 1:nrow(SecondSubstrateSet)){
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107 D835letters<-SecondSubstrateSet[i,4:18]
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108 D835letters<-D835letters[D835letters !="XXXXX"]
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109 D835letters<-paste(D835letters, sep="", collapse="")
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110 leftspaces<-c()
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111 rightspaces<-c()
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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 YYYLettersToTheLeft <- YYYposition - 1
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117 #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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118 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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119 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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120 #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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121 #variable the user puts in is
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122 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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123 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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124 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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125 #add blank spaces if the motif has less than 4 letters to the left/right
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126 motif<-c(leftspaces,YYYmotif,rightspaces)
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127 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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128 motif<-motif[!motif %in% "x"]
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129 motif<-paste(motif, sep="", collapse="")
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130 D835letters<-motif
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131 D835Ymotifs[i,1]<-D835letters
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132 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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133 }
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134 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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135 motif<-YYYmotif
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136 #add blank spaces if the motif has less than 4 letters to the left/right
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137 motif<-c(leftspaces,YYYmotif,rightspaces)
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138 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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139 motif<-motif[!motif %in% "x"]
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140 motif<-paste(motif, sep="", collapse="")
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141 D835letters<-motif
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142 D835Ymotifs[i,1]<-D835letters
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143 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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144 }
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145 }
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146 names(FTLwtmotifs)<-FTLwtAccessionNumbers
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147 names(D835Ymotifs)<-D835YAccessionNumbers
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148 }
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149 FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
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150 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
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151 D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
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152 D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
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153 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
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154 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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155 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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156 for (i in 1:nrow(FirstSubstrateSet)){
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157 FTLwtletters<-FirstSubstrateSet[i,4:18]
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158 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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159 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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160 leftspaces<-c()
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161 rightspaces<-c()
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162 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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163 YYYposition <- match(x = "x", table = YYYmotif)
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164 #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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165 #just 3 letters to the left of x
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166 YYYLettersToTheLeft <- YYYposition - 1
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167 #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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168 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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169 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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170 #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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171 #variable the user puts in is
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172 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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173 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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174 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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175 #add blank spaces if the motif has less than 4 letters to the left/right
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176 motif<-c(leftspaces,YYYmotif,rightspaces)
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177 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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|
178 motif<-motif[!motif %in% "x"]
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179 motif<-paste(motif, sep="", collapse="")
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180 FTLwtletters<-motif
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181 FTLwtmotifs[i,1]<-FTLwtletters
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182 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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183 }
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184 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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185 motif<-YYYmotif
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186 #add blank spaces if the motif has less than 4 letters to the left/right
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187 motif<-c(leftspaces,YYYmotif,rightspaces)
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188 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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|
189 motif<-motif[!motif %in% "x"]
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190 motif<-paste(motif, sep="", collapse="")
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191 FTLwtletters<-motif
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192 FTLwtmotifs[i,1]<-FTLwtletters
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193 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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194 }
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195 }
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196 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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197 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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198 for (i in 1:nrow(SecondSubstrateSet)){
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199 D835letters<-SecondSubstrateSet[i,4:18]
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200 D835letters<-D835letters[D835letters !="XXXXX"]
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201 D835letters<-paste(D835letters, sep="", collapse="")
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202 leftspaces<-c()
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203 rightspaces<-c()
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204 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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205 YYYposition <- match(x = "x", table = YYYmotif)
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206 #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
|
|
|
207 #just 3 letters to the left of x
|
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208 YYYLettersToTheLeft <- YYYposition - 1
|
|
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209 #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
|
|
|
210 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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211 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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212 #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
|
|
|
213 #variable the user puts in is
|
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214 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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215 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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216 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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217 #add blank spaces if the motif has less than 4 letters to the left/right
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218 motif<-c(leftspaces,YYYmotif,rightspaces)
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219 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
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220 motif<-motif[!motif %in% "x"]
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221 motif<-paste(motif, sep="", collapse="")
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222 D835letters<-motif
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223 D835Ymotifs[i,1]<-D835letters
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224 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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225 }
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226 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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227 motif<-YYYmotif
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228 #add blank spaces if the motif has less than 4 letters to the left/right
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229 motif<-c(leftspaces,YYYmotif,rightspaces)
|
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230 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
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|
231 motif<-motif[!motif %in% "x"]
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232 motif<-paste(motif, sep="", collapse="")
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233 D835letters<-motif
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234 D835Ymotifs[i,1]<-D835letters
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235 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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236 }
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237 }
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238 names(FTLwtmotifs)<-FTLwtAccessionNumbers
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239 names(D835Ymotifs)<-D835YAccessionNumbers
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240 }
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|
|
241 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
|
|
|
242 FullMotifsOnly_questionmark<-"NO"
|
|
|
243 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
|
|
|
244 TruncatedMotifsOnly_questionmark<-"NO"
|
|
|
245 #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)
|
|
|
246 Are_You_Looking_For_Commonality<-"NO"
|
|
|
247 #put the names of your input files here
|
|
|
248 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
|
|
|
249 Firstsubbackfreq<- read.csv("SBF1.csv", header=FALSE, stringsAsFactors=FALSE)
|
|
|
250 SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE)
|
|
|
251 Secondsubbackfreq<- read.csv("SBF2.csv", header=FALSE, stringsAsFactors=FALSE)
|
|
|
252 First_unshared_motifs_table<-"1RS.csv"
|
|
|
253 First_unshared_subbackfreq<-"1RSBF.csv"
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|
|
254 Second_unshared_motifs_table<-"2RS.csv"
|
|
|
255 Second_unshared_subbackfreq<-"2RSBF.csv"
|
|
|
256 EmptySubHeader<-FirstSubstrateSet[1,]
|
|
|
257 EmptySBFHeader<-Firstsubbackfreq[,1]
|
|
|
258 FirstCentralLetters<-FirstSubstrateSet[,11]
|
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|
259 SecondCentralLetters<-SecondSubstrateSet[,11]
|
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|
260 FirstEsses<-sapply(FirstCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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261 FirstTees<-sapply(FirstCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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262 FirstWys<-sapply(FirstCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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263 SecondEsses<-sapply(SecondCentralLetters, grepl, pattern="S", ignore.case=TRUE)
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264 SecondTees<-sapply(SecondCentralLetters, grepl, pattern="T", ignore.case=TRUE)
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265 SecondWys<-sapply(SecondCentralLetters, grepl, pattern="Y", ignore.case=TRUE)
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266 FirstCentralLetters<-replace(FirstCentralLetters,FirstEsses,"xS")
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267 FirstCentralLetters<-replace(FirstCentralLetters,FirstTees,"xT")
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268 FirstCentralLetters<-replace(FirstCentralLetters,FirstWys,"xY")
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269 SecondCentralLetters<-replace(SecondCentralLetters,SecondEsses,"xS")
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270 SecondCentralLetters<-replace(SecondCentralLetters,SecondTees,"xT")
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|
271 SecondCentralLetters<-replace(SecondCentralLetters,SecondWys,"xY")
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|
272 FirstCentralLetters->FirstSubstrateSet[,11]
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|
273 SecondCentralLetters->SecondSubstrateSet[,11]
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|
274 FirstSubstrateSet
|
|
|
275 #put the names of your input files here
|
|
|
276 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
|
|
|
277 FirstSubstrateSet
|
|
|
278 head(SecondSubstrateSet)
|
|
|
279 #put the names of your input files here
|
|
|
280 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
|
|
|
281 head(SecondSubstrateSet)
|
|
|
282 FirstSubstrateSet
|
|
|
283 #put the names of your input files here
|
|
|
284 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
|
|
|
285 FirstSubstrateSet
|
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286 #put the names of your input files here
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287 FirstSubstrateSet<- read.csv("S1.csv", stringsAsFactors=FALSE)
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288 SecondSubstrateSet<- read.csv("S2.csv", stringsAsFactors=FALSE)
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