131
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
* Estimates of genetic effects and locus genetic variance
* Estimates of genetic effects and locus genetic variance
* Estimate measures of genetic effect heterogeneities between studies
* Estimate measures of genetic effect heterogeneities between studies
== How to Generate Summary Association Statistics and Prepare Them for Meta-analysis ==
Meta-analysis summary association statistics can be generated by both RVTESTS and RAREMETALWORKER. Please refer to their documentations for generating summary association statistics
Once you have generated summary association statistics, you need to compress them with bgzip, and index them with tabix. If you use RAREMETALWORKER, the command should be like
If you use RVTESTS, your command should be
== A Simple Tutorial for Using the rareMETALS.single function ==
== A Simple Tutorial for Using the rareMETALS.single function ==
rareMETALS.single function allow you to perform meta-analyses for single variant association tests. The summary association statistics are combined using Mantel Haenszel test statistic. The details are described in our method paper Liu et al, Nat Genet, 2014.
Assume that you have a set of single variant score statistics and their covariance matrices. The examplar command can be:
score.stat.file<- c('study1.singlevar.assoc.gz','study1.singlevar.assoc.gz');
cov.file<- c('study1.singlevar.cov.gz','study1.singlevar.cov.gz');
== A Simple Tutorial for Using the rareMETALS.gene function ==
== A Simple Tutorial for Using the rareMETALS.gene function ==
