Mercurial > repos > modencode-dcc > idr_package

comparison batch-consistency-analysis.r @ 5:48767bec000d draft

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author modencode-dcc
date Thu, 17 Jan 2013 15:45:48 -0500
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4:bdd073e7ad8b 5:48767bec000d
1 ##############################################################################
2
3 # Modified 06/29/12: Kar Ming Chu
4 # Modified to work with Galaxy
5
6 # Usage: Rscript batch-consistency-analysis.r peakfile1 peakfile2 half.width overlap.ratio is.broadpeak sig.value gtable r.output overlap.output npeaks.output em.sav.output uri.sav.output
7
8 # Changes:
9 # - Appended parameter for input gnome table called gtable
10 # - Appended parameter for specifying Rout output file name (required by Galaxy)
11 # - Appended parameter for specifying Peak overlap output file name (required by Galaxy)
12 # - Appended parameter for specifying Npeak above IDR output file name (required by Galaxy)
13 # - Removed parameter outfile.prefix since main output files are replaced with strict naming
14 # - Appended parameter for specifying em.sav output file (for use with batch-consistency-plot.r)
15 # - Appended parameter for specifying uri.sav output file (for use with batch-consistency-plot.r)
16
17 ##############################################################################
18
19 # modified 3-29-10: Qunhua Li
20 # add 2 columns in the output of "-overlapped-peaks.txt": local.idr and IDR
21
22 # 01-20-2010 Qunhua Li
23 #
24 # This program performs consistency analysis for a pair of peak calling outputs
25 # It takes narrowPeak or broadPeak formats.
26 #
27 # usage: Rscript batch-consistency-analysis2.r peakfile1 peakfile2 half.width outfile.prefix overlap.ratio is.broadpeak sig.value
28 #
29 # peakfile1 and peakfile2 : the output from peak callers in narrowPeak or broadPeak format
30 # half.width: -1 if using the reported peak width,
31 # a numerical value to truncate the peaks to
32 # outfile.prefix: prefix of output file
33 # overlap.ratio: a value between 0 and 1. It controls how much overlaps two peaks need to have to be called as calling the same region. It is the ratio of overlap / short peak of the two. When setting at 0, it means as long as overlapped width >=1bp, two peaks are deemed as calling the same region.
34 # is.broadpeak: a logical value. If broadpeak is used, set as T; if narrowpeak is used, set as F
35 # sig.value: type of significant values, "q.value", "p.value" or "signal.value" (default, i.e. fold of enrichment)
36
37 args <- commandArgs(trailingOnly=T)
38
39 # consistency between peakfile1 and peakfile2
40 #input1.dir <- args[1]
41 #input2.dir <- args[2] # directories of the two input files
42 peakfile1 <- args[1]
43 peakfile2 <- args[2]
44
45 if(as.numeric(args[3])==-1){ # enter -1 when using the reported length
46 half.width <- NULL
47 }else{
48 half.width <- as.numeric(args[3])
49 }
50
51 overlap.ratio <- args[4]
52
53 if(args[5] == "T"){
54 is.broadpeak <- T
55 }else{
56 is.broadpeak <- F
57 }
58
59 sig.value <- args[6]
60
61
62 #dir1 <- "~/ENCODE/anshul/data/"
63 #dir2 <- dir1
64 #peakfile1 <- "../data/SPP.YaleRep1Gm12878Cfos.VS.Gm12878Input.PointPeak.narrowPeak"
65 #peakfile2 <- "../data/SPP.YaleRep3Gm12878Cfos.VS.Gm12878Input.PointPeak.narrowPeak"
66 #half.width <- NULL
67 #overlap.ratio <- 0.1
68 #sig.value <- "signal.value"
69
70
71 source("/mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/idr/functions-all-clayton-12-13.r")
72
73 # read the length of the chromosomes, which will be used to concatenate chr's
74 # chr.file <- "genome_table.txt"
75 # args[7] is the gtable
76 chr.file <- args[7]
77
78 chr.size <- read.table(chr.file)
79
80 # setting output files
81 r.output <- args[8]
82 overlap.output <- args[9]
83 npeaks.output <- args[10]
84 em.sav.output <- args[11]
85 uri.sav.output <- args[12]
86
87 # sink(paste(output.prefix, "-Rout.txt", sep=""))
88 sink(r.output)
89
90 ############# process the data
91 cat("is.broadpeak", is.broadpeak, "\n")
92 # process data, summit: the representation of the location of summit
93 rep1 <- process.narrowpeak(paste(peakfile1, sep=""), chr.size, half.width=half.width, summit="offset", broadpeak=is.broadpeak)
94 rep2 <- process.narrowpeak(paste(peakfile2, sep=""), chr.size, half.width=half.width, summit="offset", broadpeak=is.broadpeak)
95
96 cat(paste("read", peakfile1, ": ", nrow(rep1$data.ori), "peaks\n", nrow(rep1$data.cleaned), "peaks are left after cleaning\n", peakfile2, ": ", nrow(rep2$data.ori), "peaks\n", nrow(rep2$data.cleaned), " peaks are left after cleaning"))
97
98 if(args[3]==-1){
99 cat(paste("half.width=", "reported", "\n"))
100 }else{
101 cat(paste("half.width=", half.width, "\n"))
102 }
103 cat(paste("significant measure=", sig.value, "\n"))
104
105 # compute correspondence profile (URI)
106 uri.output <- compute.pair.uri(rep1$data.cleaned, rep2$data.cleaned, sig.value1=sig.value, sig.value2=sig.value, overlap.ratio=overlap.ratio)
107
108 #uri.output <- compute.pair.uri(rep1$data.cleaned, rep2$data.cleaned)
109
110 cat(paste("URI is done\n"))
111
112 # save output
113 # save(uri.output, file=paste(output.prefix, "-uri.sav", sep=""))
114 save(uri.output, file=uri.sav.output)
115 cat(paste("URI is saved at: ", uri.sav.output))
116
117
118 # EM procedure for inference
119 em.output <- fit.em(uri.output$data12.enrich, fix.rho2=T)
120
121 #em.output <- fit.2copula.em(uri.output$data12.enrich, fix.rho2=T, "gaussian")
122
123 cat(paste("EM is done\n\n"))
124
125 save(em.output, file=em.sav.output)
126 cat(paste("EM is saved at: ", em.sav.output))
127
128
129 # write em output into a file
130
131 cat(paste("EM estimation for the following files\n", peakfile1, "\n", peakfile2, "\n", sep=""))
132
133 print(em.output$em.fit$para)
134
135 # add on 3-29-10
136 # output both local idr and IDR
137 idr.local <- 1-em.output$em.fit$e.z
138 IDR <- c()
139 o <- order(idr.local)
140 IDR[o] <- cumsum(idr.local[o])/c(1:length(o))
141
142
143 write.out.data <- data.frame(chr1=em.output$data.pruned$sample1[, "chr"],
144 start1=em.output$data.pruned$sample1[, "start.ori"],
145 stop1=em.output$data.pruned$sample1[, "stop.ori"],
146 sig.value1=em.output$data.pruned$sample1[, "sig.value"],
147 chr2=em.output$data.pruned$sample2[, "chr"],
148 start2=em.output$data.pruned$sample2[, "start.ori"],
149 stop2=em.output$data.pruned$sample2[, "stop.ori"],
150 sig.value2=em.output$data.pruned$sample2[, "sig.value"],
151 idr.local=1-em.output$em.fit$e.z, IDR=IDR)
152
153 # write.table(write.out.data, file=paste(output.prefix, "-overlapped-peaks.txt", sep=""))
154 write.table(write.out.data, file=overlap.output)
155 cat(paste("Write overlapped peaks and local idr to: ", overlap.output, sep=""))
156
157 # number of peaks passing IDR range (0.01-0.25)
158 IDR.cutoff <- seq(0.01, 0.25, by=0.01)
159 idr.o <- order(write.out.data$idr.local)
160 idr.ordered <- write.out.data$idr.local[idr.o]
161 IDR.sum <- cumsum(idr.ordered)/c(1:length(idr.ordered))
162
163 IDR.count <- c()
164 n.cutoff <- length(IDR.cutoff)
165 for(i in 1:n.cutoff){
166 IDR.count[i] <- sum(IDR.sum <= IDR.cutoff[i])
167 }
168
169
170 # write the number of peaks passing various IDR range into a file
171 idr.cut <- data.frame(peakfile1, peakfile2, IDR.cutoff=IDR.cutoff, IDR.count=IDR.count)
172 write.table(idr.cut, file=npeaks.output, append=T, quote=F, row.names=F, col.names=F)
173 cat(paste("Write number of peaks above IDR cutoff [0.01, 0.25]: ","npeaks-aboveIDR.txt\n", sep=""))
174
175 mar.mean <- get.mar.mean(em.output$em.fit)
176
177 cat(paste("Marginal mean of two components:\n"))
178 print(mar.mean)
179
180 sink()
181
182