Gene based analysis methods, tools
1
1
Entering edit mode
3.0 years ago
zx8754 10k

Any suggestions on tool/methods for gene based analysis?

Data: I have all the GWAS data for case-control samples n=100K:

  • genotyped GWAS (~600K SNPs, maybe useful for LD)
  • imputed GWAS (IMPUTE Phase3, more SNPs)
  • meta summary data based on multiple imputed GWAS data (IMPUTE2 Phase3, maybe more power, p-values)

Aim: X, Y, and Z genes are significant when all the SNPs within the gene boundaries (with flanks?) p-values are collapsed.

I remember testing VEGAS (5-6 years ago), thought now maybe new better tools are around.

Side question, what is the suggested boundary flanks for genes, 10K, 20K? These boundaries seems silly when genes are tiny.

I would prefer to stay in R world, but happy to switch if the tool is good enough.

Let me know if you need more info.

GWAS gene methods tools R • 976 views
ADD COMMENT
1
Entering edit mode
3.0 years ago

Tools: GCTA and FAST (1.8). FAST later version is unstable with frequent crashes.

http://gcta.freeforums.net/thread/309/gcta-fastbat-based-association-analysis

For regions, it usually depends on the population and their LD pattern. You may go with 100KB on each side, or/and 250KB on each side.

For R, there's COMBAT package. It allows Vegas and one more gene-based test.

ADD COMMENT

Login before adding your answer.

Traffic: 1774 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6