Ns126:Calendar/NOTES/2016-2-18: Difference between revisions
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==Methylation Haplotype Block Plot== | ==Methylation Haplotype Block Plot== | ||
==purpose== | |||
plot MHB heatmap block | |||
===Method=== | ===Method=== | ||
*Bam2haploinfo from GWBS dataset | |||
*Merge All the haploinfo files | |||
cd /home/shg047/oasis/monod/haplo/ | cd /home/shg047/oasis/monod/haplo/ | ||
cat /home/shg047/oasis/monod/haplo/n37/*hapInfo.txt >> hapinfo.txt | cat /home/shg047/oasis/monod/haplo/n37/*hapInfo.txt >> hapinfo.txt | ||
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cat /home/shg047/oasis/monod/haplo/tumor_wgbs/*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 | 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/ | 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]] APC chr5:111986595-112228720 < /home/shg047/oasis/monod/haplo/hapinfo.txt | ||
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perl ~/oasis/monod/bin/haploinfo2LDR2.pl SHOX2 chr3:157808200-157829413 < /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 | 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 | perl [[/home/shg047/oasis/monod/bin/LDR2extent.pl]] chr5:112039140-112047142 APC.chr5.sqr > APC.full.region.sqr | ||
=== Result === | === 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 |
Latest revision as of 10:27, 26 February 2016
Methylation Haplotype Block Plot[edit]
purpose[edit]
plot MHB heatmap block
Method[edit]
- 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[edit]
- 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()
File:APC.LD.block-3.jpg File:3C45.tm.png
Conclusion[edit]
- 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