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1
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1 }
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2 }else { #filter=="relaxed"
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3 for (node in nodes){
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4 if (disc[node]==0){
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5 val=min(dfundes[,node])
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6 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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7 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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8 }
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9 if (disc[node]==1){
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10 val=max(dfdes[,node])
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11 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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12 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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13 }
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14 }
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15 }
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16 View(isdisc)
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17 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
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18 colnames(hammings)=c("replicate","perturbation")
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19 hammings$hammingdist<-apply(isdisc,1,function(x) sum(disc != x))
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20 View(hammings)
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21 is<-read.delim("internal_markers.txt",sep=" ")
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22 is$ID<-paste(is$replicate,is$perturbation,sep="_")
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23 row.names(is)<-is$ID
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24 is<- is %>% select(-ID,-perturbation,-replicate)
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25 isdisc<-is
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26 if (filter=="strict"){
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27 for (node in nodes){
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28 if (disc[node]==0){
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29 val=max(dfdes[,node])
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30 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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31 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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32 }
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33 if (disc[node]==1){
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34 val=min(dfdes[,node])
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35 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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36 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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37 }
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38 }
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39 }else { #filter=="relaxed"
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40 for (node in nodes){
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41 if (disc[node]==0){
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42 val=min(dfundes[,node])
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43 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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44 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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45 }
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46 if (disc[node]==1){
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47 val=max(dfdes[,node])
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48 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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49 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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50 }
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51 }
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52 }
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53 hammings<-data.frame(row.names(isdisc))
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54 colnames(hammings)=c("perturbations")
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55 # hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
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56 # colnames(hammings)=c("replicate","perturbation")
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57 hammings<-data.frame(row.names())
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58 hammings$hammingdist<-apply(isdisc,1,function(x) sum(disc != x))
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59 View(hammings)
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60 is<-read.delim("internal_markers.txt",sep=" ")
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61 isdisc<-is
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62 if (filter=="strict"){
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63 for (node in nodes){
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64 if (disc[node]==0){
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65 val=max(dfdes[,node])
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66 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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67 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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68 }
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69 if (disc[node]==1){
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70 val=min(dfdes[,node])
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71 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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72 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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73 }
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74 }
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|
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75 }else { #filter=="relaxed"
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76 for (node in nodes){
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77 if (disc[node]==0){
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78 val=min(dfundes[,node])
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79 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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80 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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|
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81 }
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82 if (disc[node]==1){
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83 val=max(dfdes[,node])
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84 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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85 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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86 }
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87 }
|
|
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88 }
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89 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
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90 colnames(hammings)=c("replicate","perturbation")
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91 # hammings<-data.frame(row.names())
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92 test$hammingdist<-apply(isdisc,1,function(x) sum(disc != x))
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93 # hammings<-data.frame(row.names(isdisc))
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94 # colnames(hammings)=c("perturbations")
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95 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
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96 colnames(hammings)=c("replicate","perturbation")
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97 # hammings<-data.frame(row.names(isdisc))
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98 # colnames(hammings)=c("perturbations")
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99 test<-data.frame(isdisc$replicate,isdisc$perturbation)
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100 colnames(test)=c("replicate","perturbation")
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101 # hammings<-data.frame(row.names())
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102 test$hammingdist<-apply(isdisc,1,function(x) sum(disc != x))
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103 View(test)
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104 # hammings<-data.frame(row.names(isdisc))
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105 # colnames(hammings)=c("perturbations")
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106 test<-data.frame(isdisc$replicate,isdisc$perturbation)
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107 colnames(test)=c("replicate","perturbation")
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108 # hammings<-data.frame(row.names())
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109 test$hammingdist<-apply(isdisc[,3],1,function(x) sum(disc != x))
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110 # hammings<-data.frame(row.names())
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111 test$hammingdist<-lapply(isdisc[,3],1,function(x) sum(disc != x))
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112 # hammings<-data.frame(row.names())
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113 test$hammingdist<-lapply(isdisc[,3],function(x) sum(disc != x))
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114 hammings$hammingdist<-apply(isdisc,1,function(x) sum(disc != x))
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115 if (length(nodes)<10){
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116 hams1_1<-hammings %>%filter(hammingdist<1)
|
|
|
117 }else{
|
|
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118 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
|
|
|
119 }
|
|
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120 exp<-read.delim('exp_internalmarkers.txt',sep=" ",row.names = 1)
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|
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121 samples<-read.delim("test-data/samples.txt",sep="\t",row.names = 1)
|
|
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122 exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples))
|
|
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123 desired<-"sensitive"
|
|
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124 undesired<-"resistant"
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|
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125 filter<-"strict"
|
|
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126 dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE]))
|
|
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127 meandes<- apply(dfdes,2,mean)
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|
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128 dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE]))
|
|
|
129 meandundes<-apply(dfundes,2,mean)
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|
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130 test<-meandes-meandundes
|
|
|
131 disc<-test
|
|
|
132 disc[disc<0]<-0
|
|
|
133 disc[disc>0]<-1
|
|
|
134 nodes<-colnames(dfdes)
|
|
|
135 is<-read.delim("internal_markers.txt",sep=" ")
|
|
|
136 is$ID<-paste(is$replicate,is$perturbation,sep="_")
|
|
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137 row.names(is)<-is$ID
|
|
|
138 is<- is %>% select(-ID,-perturbation,-replicate)
|
|
|
139 isdisc<-is
|
|
|
140 if (filter=="strict"){
|
|
|
141 for (node in nodes){
|
|
|
142 if (disc[node]==0){
|
|
|
143 val=max(dfdes[,node])
|
|
|
144 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
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145 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
146 }
|
|
|
147 if (disc[node]==1){
|
|
|
148 val=min(dfdes[,node])
|
|
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149 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
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150 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
151 }
|
|
|
152 }
|
|
|
153 }else { #filter=="relaxed"
|
|
|
154 for (node in nodes){
|
|
|
155 if (disc[node]==0){
|
|
|
156 val=min(dfundes[,node])
|
|
|
157 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
158 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
159 }
|
|
|
160 if (disc[node]==1){
|
|
|
161 val=max(dfdes[,node])
|
|
|
162 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
163 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
164 }
|
|
|
165 }
|
|
|
166 }
|
|
|
167 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
|
|
|
168 colnames(hammings)=c("replicate","perturbation")
|
|
|
169 hammings$hammingdist<-lapply(isdisc[,3],function(x) sum(disc != x))
|
|
|
170 #plyr::count(hammings$hammingdist)
|
|
|
171 if (length(nodes)<10){
|
|
|
172 hams1_1<-hammings %>%filter(hammingdist<1)
|
|
|
173 }else{
|
|
|
174 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
|
|
|
175 }
|
|
|
176 poi<-Reduce(intersect,list(hams1_1$perturbations))
|
|
|
177 write.table(poi,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,col.names = c('pert'))
|
|
|
178 write.table(poi,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
|
|
|
179 exp<-read.delim('exp_internalmarkers.txt',sep=" ",row.names = 1)
|
|
|
180 samples<-read.delim("test-data/samples.txt",sep="\t",row.names = 1)
|
|
|
181 exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples))
|
|
|
182 desired<-"sensitive"
|
|
|
183 undesired<-"resistant"
|
|
|
184 filter<-"strict"
|
|
|
185 dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE]))
|
|
|
186 meandes<- apply(dfdes,2,mean)
|
|
|
187 dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE]))
|
|
|
188 meandundes<-apply(dfundes,2,mean)
|
|
|
189 test<-meandes-meandundes
|
|
|
190 disc<-test
|
|
|
191 disc[disc<0]<-0
|
|
|
192 disc[disc>0]<-1
|
|
|
193 nodes<-colnames(dfdes)
|
|
|
194 is<-read.delim("internal_markers.txt",sep=" ")
|
|
|
195 is$ID<-paste(is$replicate,is$perturbation,sep="_")
|
|
|
196 row.names(is)<-is$ID
|
|
|
197 is<- is %>% select(-ID,-perturbation,-replicate)
|
|
|
198 isdisc<-is
|
|
|
199 if (filter=="strict"){
|
|
|
200 for (node in nodes){
|
|
|
201 if (disc[node]==0){
|
|
|
202 val=max(dfdes[,node])
|
|
|
203 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
204 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
205 }
|
|
|
206 if (disc[node]==1){
|
|
|
207 val=min(dfdes[,node])
|
|
|
208 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
209 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
210 }
|
|
|
211 }
|
|
|
212 }else { #filter=="relaxed"
|
|
|
213 for (node in nodes){
|
|
|
214 if (disc[node]==0){
|
|
|
215 val=min(dfundes[,node])
|
|
|
216 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
217 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
218 }
|
|
|
219 if (disc[node]==1){
|
|
|
220 val=max(dfdes[,node])
|
|
|
221 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
222 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
223 }
|
|
|
224 }
|
|
|
225 }
|
|
|
226 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
|
|
|
227 colnames(hammings)=c("replicate","perturbation")
|
|
|
228 hammings$hammingdist<-lapply(isdisc[,3],function(x) sum(disc != x))
|
|
|
229 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
|
|
|
230 colnames(hammings)=c("replicate","perturbation")
|
|
|
231 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
|
|
|
232 exp<-read.delim('exp_internalmarkers.txt',sep=" ",row.names = 1)
|
|
|
233 samples<-read.delim("test-data/samples.txt",sep="\t",row.names = 1)
|
|
|
234 exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples))
|
|
|
235 desired<-"sensitive"
|
|
|
236 undesired<-"resistant"
|
|
|
237 filter<-"strict"
|
|
|
238 dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE]))
|
|
|
239 meandes<- apply(dfdes,2,mean)
|
|
|
240 dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE]))
|
|
|
241 meandundes<-apply(dfundes,2,mean)
|
|
|
242 test<-meandes-meandundes
|
|
|
243 disc<-test
|
|
|
244 disc[disc<0]<-0
|
|
|
245 disc[disc>0]<-1
|
|
|
246 nodes<-colnames(dfdes)
|
|
|
247 is<-read.delim("internal_markers.txt",sep=" ")
|
|
|
248 isdisc<-is
|
|
|
249 if (filter=="strict"){
|
|
|
250 for (node in nodes){
|
|
|
251 if (disc[node]==0){
|
|
|
252 val=max(dfdes[,node])
|
|
|
253 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
254 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
255 }
|
|
|
256 if (disc[node]==1){
|
|
|
257 val=min(dfdes[,node])
|
|
|
258 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
259 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
260 }
|
|
|
261 }
|
|
|
262 }else { #filter=="relaxed"
|
|
|
263 for (node in nodes){
|
|
|
264 if (disc[node]==0){
|
|
|
265 val=min(dfundes[,node])
|
|
|
266 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
267 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
268 }
|
|
|
269 if (disc[node]==1){
|
|
|
270 val=max(dfdes[,node])
|
|
|
271 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
272 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
273 }
|
|
|
274 }
|
|
|
275 }
|
|
|
276 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
|
|
|
277 colnames(hammings)=c("replicate","perturbation")
|
|
|
278 hammings$hammingdist<-lapply(isdisc[,3],function(x) sum(disc != x))
|
|
|
279 #plyr::count(hammings$hammingdist)
|
|
|
280 if (length(nodes)<10){
|
|
|
281 hams1_1<-hammings %>%filter(hammingdist<1)
|
|
|
282 }else{
|
|
|
283 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
|
|
|
284 }
|
|
|
285 poi<-Reduce(intersect,list(hams1_1$perturbations))
|
|
|
286 write.table(poi,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
|
|
|
287 View(hammings)
|
|
|
288 if (length(nodes)<10){
|
|
|
289 hams1_1<-hammings %>%filter(hammingdist<1)
|
|
|
290 }else{
|
|
|
291 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
|
|
|
292 }
|
|
|
293 View(hams1_1)
|
|
|
294 poi<-Reduce(intersect,list(hams1_1$perturbations))
|
|
|
295 write.table(poi,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
|
|
|
296 source('~/Dropbox/NETISCE_galaxy/new_bin/crit2-update.R')
|
|
|
297 exp<-read.delim('exp_internalmarkers.txt',sep=" ",row.names = 1)
|
|
|
298 samples<-read.delim("test-data/samples.txt",sep="\t",row.names = 1)
|
|
|
299 exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples))
|
|
|
300 desired<-"sensitive"
|
|
|
301 undesired<-"resistant"
|
|
|
302 filter<-"strict"
|
|
|
303 dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE]))
|
|
|
304 meandes<- apply(dfdes,2,mean)
|
|
|
305 dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE]))
|
|
|
306 meandundes<-apply(dfundes,2,mean)
|
|
|
307 test<-meandes-meandundes
|
|
|
308 disc<-test
|
|
|
309 disc[disc<0]<-0
|
|
|
310 disc[disc>0]<-1
|
|
|
311 nodes<-colnames(dfdes)
|
|
|
312 is<-read.delim("internal_markers.txt",sep=" ")
|
|
|
313 isdisc<-is
|
|
|
314 if (filter=="strict"){
|
|
|
315 for (node in nodes){
|
|
|
316 if (disc[node]==0){
|
|
|
317 val=max(dfdes[,node])
|
|
|
318 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
319 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
320 }
|
|
|
321 if (disc[node]==1){
|
|
|
322 val=min(dfdes[,node])
|
|
|
323 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
324 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
325 }
|
|
|
326 }
|
|
|
327 }else { #filter=="relaxed"
|
|
|
328 for (node in nodes){
|
|
|
329 if (disc[node]==0){
|
|
|
330 val=min(dfundes[,node])
|
|
|
331 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
332 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
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333 }
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334 if (disc[node]==1){
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335 val=max(dfdes[,node])
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336 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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337 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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338 }
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339 }
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340 }
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341 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
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342 colnames(hammings)=c("replicate","perturbation")
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343 hammings$hammingdist<-lapply(isdisc[,3],function(x) sum(disc != x))
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344 #plyr::count(hammings$hammingdist)
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345 if (length(nodes)<10){
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346 hams1_1<-hammings %>%filter(hammingdist<1)
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347 }else{
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348 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
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349 }
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350 poi<-Reduce(intersect,list(hams1_1$perturbations))
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351 write.table(poi,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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352 View(hams1_1)
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353 View(hams1_1)
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354 poi<-Reduce(intersect,list(hams1_1$perturbations))
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355 poi<-hams1_1
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356 View(poi)
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357 write.table(poi,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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358 write.table(hams1_1,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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359 View(hams1_1)
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360 write.table(hams1_1,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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361 write.table(as.dataframe(hams1_1),'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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362 View(hams1_1)
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363 View(hams1_1)
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364 write.table(hams1_1,file='crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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365 class(hams1_1)
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366 .libPaths('~/R_libs_36')
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367 args = commandArgs(trailingOnly=TRUE)
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368 library(plyr)
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369 library(dplyr)
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370 library(ggplot2)
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371 library(reshape2)
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372 library(readr)
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373 getwd()
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374 exp<-read.delim('exp_internalmarkers.txt',sep=" ",row.names = 1)
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375 samples<-read.delim("test-data/samples.txt",sep="\t",row.names = 1)
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376 exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples))
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377 desired<-"sensitive"
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378 undesired<-"resistant"
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379 filter<-"strict"
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380 dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE]))
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381 meandes<- apply(dfdes,2,mean)
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382 dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE]))
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383 meandundes<-apply(dfundes,2,mean)
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384 test<-meandes-meandundes
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385 disc<-test
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386 disc[disc<0]<-0
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387 disc[disc>0]<-1
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388 nodes<-colnames(dfdes)
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389 is<-read.delim("internal_markers.txt",sep=" ")
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390 isdisc<-is
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391 if (filter=="strict"){
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392 for (node in nodes){
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393 if (disc[node]==0){
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394 val=max(dfdes[,node])
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395 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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396 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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397 }
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398 if (disc[node]==1){
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399 val=min(dfdes[,node])
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400 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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401 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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402 }
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403 }
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404 }else { #filter=="relaxed"
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405 for (node in nodes){
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406 if (disc[node]==0){
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407 val=min(dfundes[,node])
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408 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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409 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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410 }
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411 if (disc[node]==1){
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412 val=max(dfdes[,node])
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413 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
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414 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
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415 }
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416 }
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417 }
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418 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
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419 colnames(hammings)=c("replicate","perturbation")
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420 hammings$hammingdist<-lapply(isdisc[,3],function(x) sum(disc != x))
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421 #plyr::count(hammings$hammingdist)
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422 if (length(nodes)<10){
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423 hams1_1<-hammings %>%filter(hammingdist<1)
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424 }else{
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425 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
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426 }
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427 poi<-Reduce(intersect,list(hams1_1$perturbations))
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428 write.table(poi,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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429 poi<-Reduce(intersect,list(hams1_1$perturbations))
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430 View(hams1_1)
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431 write.table(hams1_1,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE)
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432 write.delim(hams1_1,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")
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433 write.table(hams1_1,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")
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434 #!/usr/bin/env Rscript
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435 .libPaths('~/R_libs_36')
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436 args = commandArgs(trailingOnly=TRUE)
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437 library(plyr)
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438 library(dplyr)
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439 library(reshape2)
|
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440 library(readr)
|
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|
441 getwd()
|
|
|
442 exp<-read.delim('exp_internalmarkers.txt',sep=" ",row.names = 1)
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|
|
443 samples<-read.delim("test-data/samples.txt",sep="\t",row.names = 1)
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|
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444 exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples))
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|
|
445 desired<-"sensitive"
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|
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446 undesired<-"resistant"
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|
|
447 filter<-"strict"
|
|
|
448 dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE]))
|
|
|
449 meandes<- apply(dfdes,2,mean)
|
|
|
450 dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE]))
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451 meandundes<-apply(dfundes,2,mean)
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452 test<-meandes-meandundes
|
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|
453 disc<-test
|
|
|
454 disc[disc<0]<-0
|
|
|
455 disc[disc>0]<-1
|
|
|
456 nodes<-colnames(dfdes)
|
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457 is<-read.delim("internal_markers.txt",sep=" ")
|
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458 isdisc<-is
|
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459 if (filter=="strict"){
|
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|
460 for (node in nodes){
|
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|
461 if (disc[node]==0){
|
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|
462 val=max(dfdes[,node])
|
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|
463 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
464 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
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465 }
|
|
|
466 if (disc[node]==1){
|
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|
467 val=min(dfdes[,node])
|
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|
468 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
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469 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
470 }
|
|
|
471 }
|
|
|
472 }else { #filter=="relaxed"
|
|
|
473 for (node in nodes){
|
|
|
474 if (disc[node]==0){
|
|
|
475 val=min(dfundes[,node])
|
|
|
476 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
477 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
478 }
|
|
|
479 if (disc[node]==1){
|
|
|
480 val=max(dfdes[,node])
|
|
|
481 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1)
|
|
|
482 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0)
|
|
|
483 }
|
|
|
484 }
|
|
|
485 }
|
|
|
486 hammings<-data.frame(isdisc$replicate,isdisc$perturbation)
|
|
|
487 colnames(hammings)=c("replicate","perturbation")
|
|
|
488 hammings$hammingdist<-lapply(isdisc[,3],function(x) sum(disc != x))
|
|
|
489 if (length(nodes)<10){
|
|
|
490 hams1_1<-hammings %>%filter(hammingdist<1)
|
|
|
491 }else{
|
|
|
492 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
|
|
|
493 }
|
|
|
494 View(hams1_1)
|
|
|
495 class(hams1_1)
|
|
|
496 write.table(hams1_1,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")
|
|
|
497 typeof(hams1_1$replicate)
|
|
|
498 typeof(hams1_1$perturbation)
|
|
|
499 ?lapply
|
|
|
500 hammings$hammingdist<-lapply(simplify=T,isdisc[,3],function(x) sum(disc != x))
|
|
|
501 hammings$hammingdist<-sapply(isdisc[,3],function(x) sum(disc != x))
|
|
|
502 if (length(nodes)<10){
|
|
|
503 hams1_1<-hammings %>%filter(hammingdist<1)
|
|
|
504 }else{
|
|
|
505 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes)))
|
|
|
506 }
|
|
|
507 write.table(hams1_1,'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")
|
|
|
508 write.table(hams1_1[c(1,2),],'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")
|
|
|
509 View(hams1_1)
|
|
|
510 View(hams1_1)
|
|
|
511 write.table(hams1_1[c(1,2),],'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")
|
|
|
512 write.table(hams1_1[,c(1,2)],'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")
|
