rareMETALS is an R-package for performing single or gene-level tests for detecting rare variant associations. For questions regarding the use of this package, please contact Dajiang Liu (dajiang at
umich dot edu) or Gonçalo Abecasis (goncalo at umich dot edu). The same methodology is also implemented in command line tools. Please see [http://genome.sph.umich.edu/wiki/Rare-Metal]
== Change Log ==
* 04/01/2015 Version 5.9 is released (not a April's fool joke)! A bug in calculating Cochran-Q statistic is fixed. A bug in conditional.rareMETALS.range.group is also fixed. No other analyses are affected.
* 01/24/2015 Version 5.8 is released, which fixed a serious bug for single variant unconditional association tests with group file. If you happen to run the analyses using rareMETALS.single.group() in version 5.7, the results are likely to be incorrect. Please rerun using version 5.8. Please note only rareMETALS.single.group function is affected. All other functions should not be affected by this error.
== Where to download ==
The R package can be downloaded from [[Media:
rareMETALS_5. 9.tar.gz | rareMETALS_5. 9.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz | refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.
== Documentation ==
cov.file <- c("study1.MetaCov.assoc.gz","study2.MetaCov.assoc.gz")
score.stat.file <- c("study1.MetaScore.assoc.gz","study2.MetaScore.assoc.gz")
res <- rareMETALS.single(score.stat.file,cov.file=NULL,range="19:11200093-11201275",alternative="two.sided",ix.gold=1,callrate.cutoff=0,hwe.cutoff=0)
== A Simple Tutorial for Using the rareMETALS.range function ==
More detailed results can be found in a list res$res.list
== A Simple Tutorial for Using the conditional.rareMETALS.range==
Conditional analyses, which can assess whether rare-variant associations are affected by nearby significant common or rare variants, use RareMETALS to perform conditional analysis for single variant tests