Ns126:Calendar/NOTES/2016-2-18: Difference between revisions

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==Methylation Haplotype Block Plot==
==Methylation Haplotype Block Plot==


===purpose==
==purpose==
# plot MHB heatmap block
plot MHB heatmap block


===Method===
===Method===
 
*Bam2haploinfo from GWBS dataset
# Bam2haploinfo from GWBS dataset
*Merge All the haploinfo files
 
 
# 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
Line 16: Line 13:
  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
*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
Line 22: Line 19:
  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
*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

50*50 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 File:3C45.tm.png

Conclusion[edit]

  1. Finish 2 script: LD R2 calculation and LD R2 plot (non-proportional and genomic location proportional[Full mode])
  2. APC: methylation haplotype block was overlapped with H3K27AC