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==Methylation Haplotype Block Plot== ==purpose== plot MHB heatmap block ===Method=== *Bam2haploinfo from GWBS dataset *Merge All the haploinfo files cd /home/shg047/oasis/monod/haplo/ cat /home/shg047/oasis/monod/haplo/n37/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/wbc/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/hesc/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/tumor_wgbs/*hapInfo.txt >> hapinfo.txt cat /home/shg047/oasis/monod/haplo/salk/*hapInfo.txt >> hapinfo.txt *Haploinfo to R-square matrix by Genomic Region cd /home/shg047/oasis/monod/haplo/ perl [[~/oasis/monod/bin/haploinfo2LDR2.pl]] APC chr5:111986595-112228720 < /home/shg047/oasis/monod/haplo/hapinfo.txt perl ~/oasis/monod/bin/haploinfo2LDR2.pl ZNF154 chr19:58206356-58222715 < /home/shg047/oasis/monod/haplo/hapinfo.txt perl ~/oasis/monod/bin/haploinfo2LDR2.pl SHOX2 chr3:157808200-157829413 < /home/shg047/oasis/monod/haplo/hapinfo.txt perl ~/oasis/monod/bin/haploinfo2LDR2.pl DIRAS3 chr1:68511645-68516481 < /home/shg047/oasis/monod/haplo/hapinfo.txt *Extent Full R-square matrix by Human Genome CpG sites perl [[/home/shg047/oasis/monod/bin/LDR2extent.pl]] chr5:112039140-112047142 APC.chr5.sqr > APC.full.region.sqr === Result === * Partial CpG Mode Figure [[File:APC.LD.block-1.jpg|50*50]] [[File:APC.LD.block-2.jpg|50*50]] * Full CpG mode Figure perl ~/oasis/monod/bin/haploinfo2LDR2.pl APC.ext chr5:112043054-112197528 < /home/shg047/oasis/monod/haplo/hapinfo.txt perl /home/shg047/bin/LDR2extent.pl chr5:112043054-112197528 APC.chr5.rsq /home/kunzhang/HsGenome/hg19/HsGenome19.CpG.positions.txt > APC.chr5.rsq.ext * R plot script library("grDevices") col=colorRampPalette(c("white", "red"))(200) M <- read.table("APC.chr5.rsq.ext") dim(M) M<-data.matrix(M) M[is.na(M)]<-0 M[lower.tri(M)] <- NA Name1<-unlist(strsplit(filename,"[.]"))[1] chr<-unlist(strsplit(filename,"[.]"))[2] start<-unlist(strsplit(colnames(M)[1],"X"))[2] end<-unlist(strsplit(colnames(M)[ncol(M)],"X"))[2] xlab=paste(Name1,"(",chr,":",start,"-",end,")",sep="") xlab=paste(Name1,"(",chr,":",112043054,"-",112197528,")",sep="") jpeg("APC.LD.block-3.jpg") image(M,col = col,xaxt="n",yaxt="n",main=xlab) dev.off() [[File:APC.LD.block-3.jpg|400px]] [[File:3C45.tm.png|400px]] ===Conclusion=== #Finish 2 script: LD R2 calculation and LD R2 plot (non-proportional and genomic location proportional[Full mode]) #APC: methylation haplotype block was overlapped with H3K27AC
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