Ns126:Calendar/NOTES/2016-2-18: Difference between revisions
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image(M,col = col,xaxt="n",yaxt="n",main=xlab) | image(M,col = col,xaxt="n",yaxt="n",main=xlab) | ||
dev.off() | dev.off() | ||
[[File:APC.LD.block-3.jpg|50*50]][[File:3C45.tm.png|30*30]] | [[File:APC.LD.block-3.jpg|50*50]] | ||
[[File:3C45.tm.png|30*30]] | |||
===Conclusion=== | ===Conclusion=== |
Revision as of 10:24, 26 February 2016
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
- 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()