Editing
Kun:LabNotes/CpgSeq/2010-7-21
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
==mQTL analysis on the Breast Cancer data== *Data used: **Methylation data: 30 samples captured with the Cpg97k probe set provided by Dinh ([[Media:0_bc_matrix.txt.gz|0_bc_matrix.txt]]); **[http://genome-tech.ucsd.edu/LabNotes/upload/large_files/294-006_FinalReport.txt.gz SNP data]: 16 Illumina 1M SNP data set generated by Beckman; *Procedure: #Filtering of DNA methylation data to select for variable Cpg sites: I calculated the STD for each site, and remove those with STD<0.1; I also removed all sites that have >20% missing values. [[Media:filterMetMatrix.txt | Script.]] #Filtering of SNP data: I removed SNPs with MAF<0.2 and those has >25% missing genotypes. [[Media:genotypeReport2Matrix.txt | Script;]] #For each CpG site, take all SNPs within 1Mb downstream and upstream, perform association test with PLINK; #Estimate p-values based on permutation; #Select CpG-SNP pairs at FDR<0.1. [[Media:mQTL_PLINK.txt| Script.]] *[[Media: mQTL_results.xls | Results]]: 34,051 pairs (26,481 SNPs; 2,762 CpG sites (15.8%))
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information