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0
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1
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2 caloffset = function(genome){
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3 total_len = sum(as.numeric(genome[,2]))
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4 offset = 0
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5 for (i in 1:nrow(genome)) {
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6 offset = c(offset,offset[i]+genome[i,2])
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7 }
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8 offset
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9 }
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10
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11 coverage = function(intervals,genome,offset,resolution) {
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12
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13 nChr = length(offset) - 1
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14 total_len = offset[nChr+1]
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15 nbin = as.integer(total_len / resolution)
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16 #cat('nbin=',nbin,'genomelen=',total_len,'\n')
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17 cov = numeric(nbin)#coverage
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18 col = numeric(nbin)#color
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19 for (i in 1:nChr) {
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20 d = x[x[,1]==as.character(genome[i,1]),2:3]
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21 if (nrow(d) > 0){
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22 #cat('dim(d)=',dim(d),'\n')
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23 d = ceiling((d+offset[i])*nbin/total_len)
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24 for (j in 1:nrow(d)){
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25 cov[d[j,1]:d[j,2]] = cov[d[j,1]:d[j,2]] + 1
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26 }
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27 }
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28 col[ceiling(offset[i]*nbin/total_len):ceiling(offset[i]*nbin/total_len)] = i
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29 }
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30 list(nbin=nbin,cov=cov)
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31 }
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32
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33 # plot coverage
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34 # res = genomeView(x,genome,100000)
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35 plotcov = function(res,genome,offset,title,uselog) {
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36 if (uselog == 'log'){
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37 res$cov = log10(res$cov+1)
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38 }
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39 ymax = max(res$cov)
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40 par(mar=c(5,5,5,1))
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41 plot(seq(length(res$cov)),res$cov,type='h',cex=0.1,cex.axis=2,cex.lab=2,cex.main=3,col=res$col,xaxt='n',main=title,xlab='chromosome',ylab='coverage',frame.plot=F,ylim=c(0,ymax))
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42 xticks = numeric(nrow(genome))
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43 for (i in 1:nrow(genome)){
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44 xticks[i] = (offset[i]+offset[i+1])/2*res$nbin/offset[length(offset)]
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45 }
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46 mtext(genome[,1],side=1,at=xticks,adj=1,las=2,col=seq(nrow(genome)))
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47 }
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48
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49 union_correlation = function(x,y){
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50 z = x>0 | y>0
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51 cor(x[z],y[z])
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52 }
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