Mercurial > repos > kyost > atac_primer_tool

annotate find_qPCR_regions.R @ 0:fd3ea97a96bc draft

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planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author kyost
date Sat, 28 Apr 2018 15:07:26 -0400
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children fbfe7b785ea7
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1 ## Command to run tool:
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2 # Rscript --vanilla find_qPCR_regions.R o.coverage.bed f9.coverage.bed lib_sizes.txt cor_cutoff cov_cutoff output_file
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3
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4 # Set up R error handling to go to stderr
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5 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
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6
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7 # Avoid crashing Galaxy with an UTF8 error on German LC settings
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9
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10 args <- commandArgs(TRUE)
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11
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12 o.coverage <- args[1]
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13 f9.coverage <- args[2]
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14 lib_sizes <- args[3]
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15 corr_cutoff <- as.numeric(args[4])
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16 cov_cutoff <- as.numeric(args[5])
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17 output_file <- args[6]
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18
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19 o.coverage.data <- read.delim(o.coverage, header=FALSE)
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20 f9.coverage.data <- read.delim(f9.coverage, header=FALSE)
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21 lib.sizes.data <- read.delim(lib_sizes, header=FALSE)
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22
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23 m <- ncol(o.coverage.data)
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24
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25 #normalize library sizes to 50 mil reads
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26 lib.sizes.data <- lib.sizes.data/50000000
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27 #normalize peak reads and spanning reads by library size
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28 o.coverage.data[,5:m] <- t(apply(o.coverage.data[,5:m], 1, function(x) x/t(lib.sizes.data)))
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29 f9.coverage.data[,5:m] <- t(apply(f9.coverage.data[,5:m], 1, function(x) x/t(lib.sizes.data)))
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30
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31 #returns list of dataframes containing windows for each peak
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32 split_coverage <- function(a) {
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33 returnlist <- list()
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34 temp <- a[1,]
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35 for (i in 2:nrow(a)) {
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36 if (temp[1,4] == strsplit(as.character(a[i,4]),"_window")[[1]][1]){
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37 temp <- rbind(temp, a[i,])
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38 }else{
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39 returnlist[[length(returnlist)+1]] <- temp
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40 temp <- a[i,]
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41 }
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42 }
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43 returnlist[[length(returnlist)+1]] <- temp
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44 return(returnlist)
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45 }
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46
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47 make_cor_plot <- function(a,b, corr_cut, cov_cut, output_file) { #a=o.coverage b=f9.coverage
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48
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49 asplit <- split_coverage(a)
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50 bsplit <- split_coverage(b)
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51
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52 combined_regions <- data.frame()
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53
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54 for (i in 1:length(asplit)){
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55 n <- nrow(asplit[[i]])-1
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56 m <- ncol(asplit[[i]])
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57
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58 a_split <- asplit[[i]]
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59 b_split <- bsplit[[i]]
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60
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61 #calculate correlation between total peak reads and spanning reads in each window
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62 corb <- data.frame(cor(t(a_split[1,5:m])
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63 , t(b_split[-1,5:m])
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64 , method = "pearson"))
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65
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66 data <- data.frame(t(corb), row.names = NULL, stringsAsFactors = FALSE)
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67
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68 data <- cbind(rep(c(1:n))
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69 , a_split[-1,1:4]
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70 , data)
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71 colnames(data)<-c("position","chr", "start", "stop", "name", "correlation")
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72 rownames(data)<-NULL
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73 a_split$average <- rowMeans(a_split[,5:m])
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74 b_split$average <- rowMeans(b_split[,5:m])
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75 data2 <- data.frame(cbind(c(1:n), a_split[-1,m+1]), stringsAsFactors=FALSE)
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76 data3 <- data.frame(cbind(c(1:n), b_split[-1,m+1]), stringsAsFactors=FALSE)
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77 colnames(data2)<-c("position","averageReadDepth")
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78 colnames(data3)<-c("position","averageReadDepth")
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79
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80 #keep windows for which correlation with total peak reads is above threshold and
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81 #number of spanning reads is above cutoff
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82 regions <- data[which(data$correlation > corr_cut & data3$averageReadDepth > cov_cut),]
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83 regions <- regions[,2:4]
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84
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85 #collapse windows to non-overlappin regions
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86 if (nrow(regions)>0){
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87 regions$V4 <- paste(as.character(a_split[1,4]),"_region1",sep="")
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88 collapsed_regions <- regions[1,]
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89 nregion <- 1
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90 if (nrow(regions)>=2){
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91 for (j in 2:nrow(regions)) {
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92 if (as.numeric(regions[j,2]) <= (as.numeric(regions[j-1,3]))) {
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93 collapsed_regions[nrow(collapsed_regions),3] <- regions[j,3]
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94 }else{
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95 collapsed_regions <- rbind(collapsed_regions, regions[j,])
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96 nregion <- nregion + 1
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97 collapsed_regions[nrow(collapsed_regions),4] <- paste(as.character(a_split[1,4])
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98 ,"_region"
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99 , as.character(nregion)
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100 ,sep="")
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101 }
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102 }
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103 }
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104 rownames(collapsed_regions) <- NULL
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105
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106 combined_regions <- rbind(combined_regions, collapsed_regions)
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107 }
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108
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109
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110 }
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111
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112 write.table(combined_regions
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113 , output_file
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114 , sep = "\t"
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115 , col.names = FALSE
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116 , row.names = FALSE
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117 , quote = FALSE)
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118 print("Successfully found optimal ATAC-qPCR regions.")
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119 }
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120
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121 make_cor_plot(o.coverage.data, f9.coverage.data, corr_cutoff, cov_cutoff, output_file)