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1 TAB <- read.csv("input.csv")
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2 mysamples <- lapply(TAB$ID,function(x)getGEO(x))
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3 input <- function(TAB) { if(is(TAB, "csv")){
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4 TAB <- read.csv("input.csv")}
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5 else{
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6 print("error in data file")
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7 }}
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8 input()
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9 TAB <- read.csv("input.csv")}
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10 TAB <- read.csv("input.csv")
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11 test_func <- function(
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12 clusterSize=2,
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13 cutoff=0.2,
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14 platform_id='HM450',
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15 genome_id='hg19')
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16 {
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17 args = commandArgs(trailingOnly=TRUE)
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18 methyl_file = args[1]
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19 ChiPseq_file = args[2]
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20 output_file = args[3]
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21 options(warn=-1)
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22 TAB=read.csv(methyl_file)
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23 ChiPseq=import(ChiPseq_file)
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24 if(is.null(TAB)){
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25 stop("Must specify input files")
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26 }else{
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27 mysamples <- lapply(TAB$ID,function(x) getGEO(x))
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28 }
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29 wrappedFunction <- function(test_func)
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30 s0 <- lapply(mysamples,Table)
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31 id_ref<-lapply(s0,function(x)x$ID_REF)
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32 if(length(unique(id_ref)) != 1) {
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33 stop("Error different ID_REF for samples")
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34 } else if (is.null((unlist(unique(id_ref))))) {
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35 stop("NO GSM data avaliable")
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36 } else {
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37 values<-do.call("cbind",lapply(s0,function(x)x$VALUE))
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38 colnames(values)=TAB$ID
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39 rownames(values)=id_ref[[1]]
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40 cg <- rownames(values)
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41 probe <- c(cg)
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42 hm450.hg19 <- getPlatform(platform=platform_id, genome=genome_id)
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43 probe.info <- hm450.hg19[probe]
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44 f <- data.table(probe=names(probe.info),CHR=as.data.frame(probe.info@seqnames)$value,
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45 BP=as.numeric(probe.info@elementMetadata$probeStart))
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46 designMatrix <- model.matrix(~ TAB$Phenotype)
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47 DMR <- bumphunter(values, design = designMatrix,
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48 pos=f$BP,cutoff=cutoff,chr=f$CHR)
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49 MAT <- DMR$table[which(DMR$table$L>=clusterSize),]
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50 METH <- GRanges(seqnames=MAT$chr,
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51 ranges=IRanges
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52 (start=MAT$start,
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53 end=MAT$end),
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54 value_pos=MAT$value)
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55 peaks<-findOverlapsOfPeaks(probe.info,ChiPseq,maxgap=5000)
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56 p <- peaks$peaklist$`probe.info///ChiPseq`
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57 peakAnno <- annotatePeak(p, file=peakAnno)
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58 output_file <- annotatePeak(p, file=output_file)
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59 }}
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60 test_func <- function(
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61 clusterSize=2,
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62 cutoff=0.2,
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63 platform_id='HM450',
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64 genome_id='hg19')
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65 {
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66 args = commandArgs(trailingOnly=TRUE)
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67 methyl_file = args[1]
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68 ChiPseq_file = args[2]
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69 output_file = args[3]
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70 options(warn=-1)
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71 TAB=read.csv(methyl_file)
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72 ChiPseq=import(ChiPseq_file)
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73 if(is.null(TAB)){
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74 stop("Must specify input files")
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75 }else{
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76 mysamples <- lapply(TAB$ID,function(x) getGEO(x))
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77 }
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78 wrappedFunction <- function(test_func)
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79 s0 <- lapply(mysamples,Table)
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80 id_ref<-lapply(s0,function(x)x$ID_REF)
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81 if(length(unique(id_ref)) != 1) {
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82 stop("Error different ID_REF for samples")
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83 } else if (is.null((unlist(unique(id_ref))))) {
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84 stop("NO GSM data avaliable")
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85 } else {
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86 values<-do.call("cbind",lapply(s0,function(x)x$VALUE))
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87 colnames(values)=TAB$ID
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88 rownames(values)=id_ref[[1]]
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89 cg <- rownames(values)
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90 probe <- c(cg)
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91 hm450.hg19 <- getPlatform(platform=platform_id, genome=genome_id)
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92 probe.info <- hm450.hg19[probe]
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93 f <- data.table(probe=names(probe.info),CHR=as.data.frame(probe.info@seqnames)$value,
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94 BP=as.numeric(probe.info@elementMetadata$probeStart))
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95 designMatrix <- model.matrix(~ TAB$Phenotype)
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96 DMR <- bumphunter(values, design = designMatrix,
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97 pos=f$BP,cutoff=cutoff,chr=f$CHR)
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98 MAT <- DMR$table[which(DMR$table$L>=clusterSize),]
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99 METH <- GRanges(seqnames=MAT$chr,
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100 ranges=IRanges
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101 (start=MAT$start,
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102 end=MAT$end),
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103 value_pos=MAT$value)
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104 peaks<-findOverlapsOfPeaks(probe.info,ChiPseq,maxgap=5000)
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105 p <- peaks$peaklist$`probe.info///ChiPseq`
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106 peakAnno <- annotatePeak(p, file=peakAnno)
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107 output_file <- annotatePeak(p, file=output_file)
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108 }}
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109 )
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110 a<-c(3.2,3.7,3.6,3.9,3.7,3.5,3.8,4,3.5)
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111 a<-c(3.2,3.7,3.6,3.9,3.7,3.5,3.8,4,3.5)
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112 b<-c(2.9,2.7,2,6,2.7,2.5,2.5,3.2,3.1,3.3,2.8)
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113 a-b
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114 file<-read.csv("~/Documents/SS2.csv")
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115 head(file)
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116 e
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117 file
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118 t.test(file$WBT,file$WBA)
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119 t.test(file$WBT,file$WBA,paired=TRUE)
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120 mysamples <- lapply(TAB$ID,function(x) TablegetGEO(x))
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121 require("GEOquery",quietly = TRUE)
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122 require("BiocGenerics",quietly = TRUE)
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123 args <- commandArgs(trailingOnly = TRUE)
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124 csv_file = args[1]
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125 #csv_file <- ("test-data/input.csv")
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126 TAB=read.csv(csv_file)
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127 if(is.null(TAB)){
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128 stop("Must specify input files")
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129 }else{
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130 mysamples <- lapply(TAB$ID,function(x) TablegetGEO(x))
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131 }
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132 csv_file <- ("test-data/input.csv")
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133 TAB=read.csv(csv_file)
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134 figure = args[3]
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135 upsetplot(anno, vennpie=TRUE)
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136 dev.copy(png,'fig.png')
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137 png(upsetplot(anno, vennpie=TRUE))
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138 upsetplot(anno, vennpie=TRUE)
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139 require("ChIPseeker",quietly = TRUE)
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140 require("ChIPpeakAnno",quietly = TRUE)
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141 upsetplot(anno, vennpie=TRUE)
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142 figure<-('test-data/figure.png')
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143 anno <- annotatePeak(peaks,level="gene", annoDb="org.Hs.eg.db" )
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144 input=read.table(input,header = FALSE, sep="\t",stringsAsFactors=FALSE, quote="")
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145 input<-("test-data/bump.bed")
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146 input=read.table(input,header = FALSE, sep="\t",stringsAsFactors=FALSE, quote="")
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147 peaks <- GRanges(seqnames=input[,1],ranges=IRanges
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148 (start=input[,2],end= input[,3]))
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149 anno <- annotatePeak(peaks,level="gene", annoDb="org.Hs.eg.db" )
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150 peakAnno_genes <- as.data.frame(anno)
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151 upsetplot(anno, vennpie=TRUE)
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152 figure<-('test-data/figure.png')
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153 png(figure)
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154 dev.off()
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155 png(figure)
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156 upsetplot(anno, vennpie=TRUE)
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1
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157 org.Hs.eg.db
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158 ??org.Hs.eg.db
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159 require("ChIPseeker", quietly = TRUE)
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160 require("ChIPpeakAnno", quietly = TRUE)
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161 DMRInfo = read.table(
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162 DMR,
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163 header = FALSE,
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164 sep = "\t",
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165 stringsAsFactors = FALSE,
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166 quote = ""
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167 )
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168 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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169 ranges = IRanges
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170 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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171 annotatePeak <-
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172 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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173 ??org.Hs.eg.db
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3
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174 DMR <- ("test-data/DMR.bed")
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175 DMRInfo = read.table(
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176 DMR,
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177 header = FALSE,
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178 sep = "\t",
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179 stringsAsFactors = FALSE,
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180 quote = ""
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181 )
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182 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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183 ranges = IRanges
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184 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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185 ??GRanges
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186 require("GenomicRanges", quietly = TRUE)
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187 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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188 ranges = IRanges
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189 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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190 annotatePeak <-
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191 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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192 require("ChIPseeker", quietly = TRUE)
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193 require("ChIPpeakAnno", quietly = TRUE)
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194 annotatePeak <-
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195 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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196 annotatePeak <-
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197 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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198 write.csv(as.data.frame(annotatePeak), annoPeakTable, row.names = FALSE)
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199 DMR <- ("test-data/DMR.bed")
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200 DMRInfo = read.table(
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201 DMR,
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202 header = FALSE,
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203 sep = "\t",
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204 stringsAsFactors = FALSE,
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205 quote = ""
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206 )
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207 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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208 ranges = IRanges
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209 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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210 ranges = IRanges
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211 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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212 ??GRanges
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213 options(warn = -1)
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214 args <- commandArgs(trailingOnly = TRUE)
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215 DMR = args[1]
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216 annoPeakTable = args[2]
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217 DMR <- ("test-data/DMR.bed")
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218 DMRInfo = read.table(
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219 DMR,
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220 header = FALSE,
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221 sep = "\t",
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222 stringsAsFactors = FALSE,
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223 quote = ""
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224 )
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225 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
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226 ranges = IRanges
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227 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
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228 ??GRanges
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229 annotatePeak <-
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230 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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4
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231 annotatePeak <- as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
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