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comparison ezBAMQC/test-data/output/data/smp0.mapq_profile.r @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 png("/sonas-hs/bsr/hpc/data/yjin/test_BAMqc/exp/test1/figs/smp0.mapq_profile.png",width=500,height=500,units="px")
2 mapq_val=c(0,1,3,255)
3 mapq_count=c(573,3442,9322,64349)
4 xname=c("<3","<10","<20","<30","30-255")
5 freq = rep(0,5)
6 freq[1] = sum(mapq_count[which(mapq_val<3)])/77686*100
7 freq[2] = sum(mapq_count[which(mapq_val<10)])/77686*100
8 freq[3] = sum(mapq_count[which(mapq_val<20)])/77686*100
9 freq[4] = sum(mapq_count[which(mapq_val<30)])/77686*100
10 freq[5] = 100
11 barplot(freq,beside=T,xlab="Mapping Quality",border="NA",space=1.5,main="Mapping Quality",ylim=c(0,100),ylab="Cumulative proportion (%)",col="blue",names.arg=xname)
12 dev.state=dev.off()