Gene based analysis methods, tools
Entering edit mode
5.5 years ago
zx8754 11k

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 R • 1.4k views
Entering edit mode
5.5 years ago

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

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.


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