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1 #!/usr/bin/Rscript --vanilla
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2 library(getopt)
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3 spec <- matrix(c("help", "h", 0, "logical", "view this help", "segfile1", "s", 1, "character", "seg file 1", "segfile2", "t", 1, "character", "seg file 2", "output", "o", 1, "character", "output file", "fdr", "f", 2, "character", paste("fdr method [", paste(p.adjust.methods, collapse="|"), "]", sep=""),
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4 "reference", "r", 2, "character", "reference to use [b37|hg19|GRCh37|mm9|NCBIM37|mm10|GRCm38|dm3|BDGP5]", "annot", "a", 2, "character", "annotation to add [both|gene|cpg]", "processes", "p", 2, "integer", "number of cluster instances to open [1]"), ncol=5, byrow=T)
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5 opt <- getopt(spec)
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6
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7 # set default options
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8 if(is.null(opt$fdr)) opt$fdr <- "BH"
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9 if(is.null(opt$reference)) opt$reference <- "hg19"
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10 if(is.null(opt$annot)) opt$annot <- "both"
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11 if(is.null(opt$processes)) opt$processes <- 1
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12
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13 # check if any invalid options
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14 if(! opt$annot %in% c("both", "gene", "cpg") || !opt$fdr %in% p.adjust.methods || !opt$reference %in% c("b37", "hg19", "GRCh37", "mm9", "NCBIM37", "mm10", "GRCm38", "dm3", "BDGP5")) {
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15 opt$help <- 1
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16 }
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17
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18 # print help file if any incorrect
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19 if(!is.null(opt$help) || is.null(opt$segfile1) || is.null(opt$output) || is.null(opt$output) || is.na(opt$processes)) {
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20 self = commandArgs()[1];
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21 cat(getopt(spec, usage=T, command="differential_methylation.R"))
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22 q(status=1)
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23 }
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24
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25 library(snow)
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26 cl <- makeCluster(opt$p, type = "MPI")
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27
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28 segfile1 <- read.table(opt$segfile1, sep="\t", as.is=T, head=T, quote = "")
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29 segfile2 <- read.table(opt$segfile2, sep="\t", as.is=T, head=T, quote = "")
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30
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31 rownames(segfile1) <- paste(segfile1[,2], ":", segfile1[,3], "-", segfile1[,4], sep="")
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32 rownames(segfile2) <- paste(segfile2[,2], ":", segfile2[,3], "-", segfile2[,4], sep="")
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33
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34 common_reg <- intersect(rownames(segfile1), rownames(segfile2))
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35 prop_test <- function(x, n, fdr) {
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36 library(abind)
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37 ESTIMATE <- x/n
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38 DELTA <- ESTIMATE[,1L] - ESTIMATE[,2L]
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39 YATES <- pmin(abs(DELTA)/rowSums(1/n), 0.5)
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40 p <- rowSums(x)/rowSums(n)
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41 df <- 1
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42 x <- abind(x, n - x, along=3)
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43 E <- abind(n*p, n*(1-p), along=3)
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44 STATISTIC <- rowSums((abs(x - E) - YATES)^2/E)
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45 STATISTIC[is.na(STATISTIC)] <- 0
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46 PVAL <- pchisq(STATISTIC, df, lower.tail = FALSE)
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47 return(data.frame(X_Squared = round(STATISTIC, 3), P.value= round(PVAL, 6), P.adjusted = round(p.adjust(PVAL, method=fdr), 6)))
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48 }
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49 results <- prop_test(cbind(segfile1[common_reg, "Methylated"], segfile2[common_reg, "Methylated"]), cbind(segfile1[common_reg, "Total"], segfile2[common_reg, "Total"]), opt$fdr)
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50
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51 sample1 <- segfile1[1, 1]
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52 sample2 <- segfile2[1, 1]
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53 tab_out <- data.frame(ID = paste(sample1, "vs", sample2, sep="."), segfile1[common_reg, c(2:4)], segfile1[common_reg, c("Methylated", "Total", "FractionMethylated")],
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54 segfile2[common_reg, c("Methylated", "Total", "FractionMethylated")], results, DiffProp = round(segfile1[common_reg, "FractionMethylated"] - segfile2[common_reg, "FractionMethylated"], 6), stringsAsFactors=F)
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55 colnames(tab_out)[c(5:10)] <- c(paste(sample1, "Methylated", sep="."), paste(sample1, "Total", sep="."), paste(sample1, "Proportion", sep="."), paste(sample2, "Methylated", sep="."),
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56 paste(sample2, "Total", sep="."), paste(sample2, "Proportion", sep="."))
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57
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58 rm(segfile1)
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59 rm(segfile2)
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60 gc()
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61
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62 add_annot <- function(tab, annotation, genome) {
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63 # find closest feature
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64 if(genome == "hg19" || genome == "GRCh37" || genome == "b37") {
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65 genome <- "hg19"
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66 dataset <- "hsapiens_gene_ensembl"
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67 biomart <- "ensembl"
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68 host <- "www.biomart.org"
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69 attributes <- c("ensembl_gene_id", "hgnc_symbol", "refseq_mrna", "start_position", "end_position")
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70 } else if(genome == "mm9" || genome == "NCBIM37") {
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71 genome <- "mm9"
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72 dataset <- "mmusculus_gene_ensembl"
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73 biomart <- "ENSEMBL_MART_ENSEMBL"
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74 host <- "may2012.archive.ensembl.org"
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75 attributes <- c("ensembl_gene_id", "mgi_symbol", "refseq_mrna", "start_position", "end_position")
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76 } else if(genome == "mm10" || genome == "GRCm38") {
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77 genome <- "mm10"
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78 dataset <- "mmusculus_gene_ensembl"
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79 biomart <- "ensembl"
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80 host <- "www.biomart.org"
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81 attributes <- c("ensembl_gene_id", "mgi_symbol", "refseq_mrna", "start_position", "end_position")
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82 } else if(genome == "dm3" || genome == "BDGP5") {
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83 genome <- "dm3"
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84 dataset <- "dmelanogaster_gene_ensembl"
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85 biomart <- "ensembl"
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86 host <- "www.biomart.org"
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87 attributes <- c("ensembl_gene_id", "flybasecgid_gene", "refseq_mrna", "start_position", "end_position")
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88 }
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89
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90 e_to_U = c("GL000191.1" = "1_gl000191_random", "GL000192.1" = "1_gl000192_random", "GL000193.1" = "4_gl000193_random", "GL000194.1" = "4_gl000194_random",
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91 "GL000195.1" = "7_gl000195_random", "GL000196.1" = "8_gl000196_random", "GL000197.1" = "8_gl000197_random", "GL000198.1" = "9_gl000198_random",
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92 "GL000199.1" = "9_gl000199_random", "GL000200.1" = "9_gl000200_random", "GL000201.1" = "9_gl000201_random", "GL000202.1" = "11_gl000202_random",
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93 "GL000203.1" = "17_gl000203_random", "GL000204.1" = "17_gl000204_random", "GL000205.1" = "17_gl000205_random", "GL000206.1" = "17_gl000206_random",
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94 "GL000207.1" = "18_gl000207_random", "GL000208.1" = "19_gl000208_random", "GL000209.1" = "19_gl000209_random", "GL000210.1" = "21_gl000210_random",
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95 "GL000211.1" = "Un_gl000211", "GL000212.1" = "Un_gl000212", "GL000213.1" = "Un_gl000213", "GL000214.1" = "Un_gl000214",
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96 "GL000215.1" = "Un_gl000215", "GL000216.1" = "Un_gl000216", "GL000217.1" = "Un_gl000217", "GL000218.1" = "Un_gl000218",
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97 "GL000219.1" = "Un_gl000219", "GL000220.1" = "Un_gl000220", "GL000221.1" = "Un_gl000221", "GL000222.1" = "Un_gl000222",
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98 "GL000223.1" = "Un_gl000223", "GL000224.1" = "Un_gl000224", "GL000225.1" = "Un_gl000225", "GL000226.1" = "Un_gl000226",
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99 "GL000227.1" = "Un_gl000227", "GL000228.1" = "Un_gl000228", "GL000229.1" = "Un_gl000229", "GL000230.1" = "Un_gl000230",
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100 "GL000231.1" = "Un_gl000231", "GL000232.1" = "Un_gl000232", "GL000233.1" = "Un_gl000233", "GL000234.1" = "Un_gl000234",
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101 "GL000235.1" = "Un_gl000235", "GL000236.1" = "Un_gl000236", "GL000237.1" = "Un_gl000237", "GL000238.1" = "Un_gl000238",
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102 "GL000239.1" = "Un_gl000239", "GL000240.1" = "Un_gl000240", "GL000241.1" = "Un_gl000241", "GL000242.1" = "Un_gl000242",
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103 "GL000243.1" = "Un_gl000243", "GL000244.1" = "Un_gl000244", "GL000245.1" = "Un_gl000245", "GL000246.1" = "Un_gl000246",
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104 "GL000247.1" = "Un_gl000247", "GL000248.1" = "Un_gl000248", "GL000249.1" = "Un_gl000249")
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105
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106 # function to conver ucsc chroms to ensembl
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107 ensembl <- function(chr, genome) {
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108 # ensembl does not us chr and M is MT
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109 chr <- sub("^chr", "", chr)
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110 if(genome == "dm3" || genome == "BDGP5") {
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111 chr <- sub("^M$", "dmel_mitochondrion_genome", chr)
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112 } else {
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113 chr <- sub("^M$", "MT", chr)
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114 }
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115 chr[which(chr %in% e_to_U)] <- names(e_to_U)[match(chr[which(chr %in% e_to_U)], e_to_U)]
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116 return(chr)
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117 }
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118
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119 # function to conver ensembl chroms to ucsc
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120 ucsc <- function(chr) {
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121 chr <- sub("^chr", "", chr)
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122 tmp <- which(chr %in% names(c(e_to_U, dmel_mitochondrion_genome = "M", MT = "M")))
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123 chr[tmp] <- c(e_to_U, dmel_mitochondrion_genome = "M", MT = "M")[chr[tmp]]
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124 paste("chr", chr, sep="")
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125 }
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126
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127 # function to get the gene annotation by chromosome
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128 get_genes <- function(chr) {
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129 library(biomaRt)
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130 mart <- useMart(biomart=biomart, dataset=dataset, host=host)
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131 tab <- getBM(attributes = attributes, filters = "chromosome_name", values = chr, mart = mart)
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132 if(any(is.na(tab))) for(i in 1:ncol(tab)) tab[is.na(tab[,i]), i] <- ""
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133 mult_ids <- names(which(table(tab$ensembl_gene_id) > 1))
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134 rem <- NULL
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135 for(i in mult_ids) {
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136 index <- which(tab$ensembl_gene_id == i)
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137 refseq <- which(tab$ensembl_gene_id == i & tab$refseq_mrna != "")
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138 if(length(refseq) > 0) {
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139 rem <- c(rem, setdiff(index, refseq[1]))
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140 } else {
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141 rem <- c(rem, index[-1])
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142 }
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143 }
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144 if(length(rem) > 0) tab <- tab[-rem,]
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145 colnames(tab)[4:5] <- c("feature_start", "feature_end")
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146 return(tab)
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147 }
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148
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149 get_cpg <- function(chr) {
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150 library(rtracklayer)
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151 options(stringsAsFactors=F)
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152 session <- browserSession()
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153 genome(session) <- genome
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154 query <- ucscTableQuery(session, "CpG Islands", GRangesForUCSCGenome(genome, chr))
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155 cpg <- getTable(query)
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156 cpg <- cpg[, c("name", "perCpg", "perGc", "chromStart", "chromEnd")]
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157 colnames(cpg) <- c("cpg", "cpg_perCpg", "cpg_perGc", "cpg_start", "cpg_end")
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158 return(cpg)
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159 }
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160 chr <- tab[1, 2]
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161
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162 # get the gene info for this chrom
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163 if(annotation == "gene") {
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164 tab <- cbind(tab, ensembl_gene_id = "", id = "", refseq_mrna = "", feature_start = "", feature_end = "", Distance_To_Feature = "", stringsAsFactors=F)
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165 annotData <- get_genes(ensembl(chr, genome))
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166 colnames(tab)[16] <- attributes[2]
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167 } else {
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168 tab <- cbind(tab, cpg = "", cpg_perCpg = "", cpg_perGc = "", cpg_start = "", cpg_end = "", Distance_To_cpg = "", stringsAsFactors=F)
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169 annotData <- get_cpg(ucsc(chr))
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170 }
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171 if(nrow(annotData) == 0) return(tab)
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172
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173 starts <- t(matrix(cbind(-1, as.numeric(annotData[, 4])), ncol=2, byrow=F))
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174 ends <- t(matrix(cbind(-1, as.numeric(annotData[, 5])), ncol=2, byrow=F))
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175
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176 # calculate the distances from the features to the regions
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177 dist_start_start <- matrix(cbind(tab$loc.start, 1), ncol=2, byrow=F) %*% starts
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178 dist_start_end <- matrix(cbind(tab$loc.start, 1), ncol=2, byrow=F) %*% ends
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179 dist_end_start <- matrix(cbind(tab$loc.end, 1), ncol=2, byrow=F) %*% starts
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180 dist_end_end <- matrix(cbind(tab$loc.end, 1), ncol=2, byrow=F) %*% ends
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181
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182 # determine which regions overlap at least 1 feature
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183 sum_signs <- abs(sign(dist_start_start) + sign(dist_start_end) + sign(dist_end_start) + sign(dist_end_end))
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184 regions <- which(sum_signs != 4, arr.ind=TRUE)
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185 if(length(regions) > 0) {
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186 overlap <- sort(unique(regions[,1]))
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187 non_overlap <- c(1:nrow(tab))[-overlap]
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188 } else {
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189 overlap <- NULL
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190 non_overlap <- c(1:nrow(tab))
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191 }
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192
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193 # reduce to regions with no overlaping feqature
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194 if(length(overlap) > 0) {
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195 dist_start_start <- matrix(dist_start_start[non_overlap,], ncol=ncol(dist_start_start))
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196 dist_start_end <- matrix(dist_start_end[non_overlap,], ncol=ncol(dist_start_end))
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197 dist_end_start <- matrix(dist_end_start[non_overlap,], ncol=ncol(dist_end_start))
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198 dist_end_end <- matrix(dist_end_end[non_overlap,], ncol=ncol(dist_end_end))
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199 }
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200
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201 rm(sum_signs)
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202 gc()
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203
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204 # extract the annot for the regions with overlaping features
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205 if(length(overlap) > 0) {
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206 annot <- sapply(overlap, function(x, y) {
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207 x <- regions[which(regions[,1] == x), 2]
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208 sub("^//$", "", c(paste(annotData[x,1], collapse="//"), paste(annotData[x,2], collapse="//"), paste(annotData[x,3], collapse="//"), paste(annotData[x,4], collapse="//"), paste(annotData[x,5], collapse="//")))
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209 }, regions)
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210 annot <- as.data.frame(t(annot), stringsAsFactors=F)
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211 annot <- cbind(annot, "Overlap", stringsAsFactors=F)
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212 colnames(annot) <- c(colnames(annotData), tail(colnames(tab),1))
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213 }
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214 rm(regions)
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215 gc()
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216
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217 # for non the non-overlaps the distance of the closest features to each region
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218 if(length(non_overlap) > 0) {
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219 clst_pts <- matrix(0, ncol=4, nrow=length(non_overlap))
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220 clst_pts[,1] <- max.col(-abs(dist_start_start), "last")
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221 clst_pts[,2] <- max.col(-abs(dist_start_end), "last")
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222 clst_pts[,3] <- max.col(-abs(dist_end_start), "last")
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223 clst_pts[,4] <- max.col(-abs(dist_end_end), "last")
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224 dist <- matrix(0, ncol=4, nrow=length(non_overlap))
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225 if(length(clst_pts[,1]) == 1) {
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226 dist[,1] <- dist_start_start[1, clst_pts[,1]]
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227 dist[,2] <- dist_start_end[1, clst_pts[,2]]
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228 dist[,3] <- dist_end_start[1, clst_pts[,3]]
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229 dist[,4] <- dist_end_end[1, clst_pts[,4]]
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230
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231 # extract the annot for the regions with non-overlaping features
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232 clst_all <- max.col(-abs(dist))
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233 dist_to_feat <- dist[1, clst_all]
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234 clst <- clst_pts[1, clst_all]
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235 } else {
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236 dist[,1] <- dist_start_start[cbind(seq(clst_pts[,1]), clst_pts[,1])]
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237 dist[,2] <- dist_start_end[cbind(seq(clst_pts[,2]), clst_pts[,2])]
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238 dist[,3] <- dist_end_start[cbind(seq(clst_pts[,3]), clst_pts[,3])]
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239 dist[,4] <- dist_end_end[cbind(seq(clst_pts[,4]), clst_pts[,4])]
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240
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241 # extract the annot for the regions with non-overlaping features
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242 clst_all <- max.col(-abs(dist))
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243 dist_to_feat <- dist[cbind(seq(clst_all), clst_all)]
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244 clst <- clst_pts[cbind(seq(clst_all), clst_all)]
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245 }
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246 annot_non_overlap <- cbind(annotData[clst, ], dist_to_feat)
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247 colnames(annot_non_overlap) <- c(colnames(annotData), tail(colnames(tab),1))
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248 }
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249
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250 rm(dist_start_start)
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251 rm(dist_start_end)
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252 rm(dist_end_start)
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253 rm(dist_end_end)
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254 gc()
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255
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256 if(length(overlap) > 0) tab[overlap, colnames(annot)] <- annot
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257 if(length(non_overlap) > 0) tab[non_overlap, colnames(annot_non_overlap)] <- annot_non_overlap
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258 return(tab)
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259 }
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260
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261 tab_list <- list()
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262 for(i in unique(tab_out[,2])) tab_list[[i]] <- tab_out[which(tab_out$chrom == i),]
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263 rm(tab_out)
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264 gc()
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265 if(opt$annot == "both" || opt$annot == "gene") {
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266 annotation <- "gene"
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267 tab_list <- clusterApplyLB(cl, tab_list, add_annot, annotation, opt$reference)
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268 }
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269
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270 if(opt$annot == "both" || opt$annot == "cpg") {
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271 annotation <- "cpg"
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272 tab_list <- clusterApplyLB(cl, tab_list, add_annot, annotation, opt$reference)
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273 }
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274
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275 tab_out <- NULL
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276 for(i in 1:length(tab_list)) tab_out <- rbind(tab_out, tab_list[[i]])
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277
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278 cat("'", file=opt$output)
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279 write.table(tab_out[,c(1:13, 15:26, 14)], opt$output, row.names=F, col.names=T, quote=F, sep="\t", append=T)
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280 stopCluster(cl)
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281 q(status=0)
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