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RareMETALS

33 bytes added, 21:16, 24 March 2015
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* Estimate measures of genetic effect heterogeneities between studies
== Exemplar Dataset==
Four datasets are useful to get you started on how to use rareMETALS R package for meta-analyses of gene-level association test
If you use RVTESTS, your command should be
: bgzip study1.MetaScore.assoc
: tabix -s 1 -b 2 -e 2 -S 1 study1.MetaScore.assoc.gz
: tabix -s 1 -b 2 -e 2 -S 1 study1.MetaCov.assoc.gz
== A Simple Tutorial for Using the rareMETALS.single function ==
Example:
library(rareMETALS) 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);
score.stat.file <- c("study1.MetaScore.assoc.gz","study2.MetaScore.assoc.gz") res <- == A Simple Tutorial for Using the rareMETALS.single(score.stat.file,cov.file=NULL,rangefunction ="19:11200093-11201275",alternative="two.sided",ix.gold=1,callrate.cutoff=0,hwe.cutoff=0);
res <- rareMETALS.range(score.stat.file,cov.file,range="19:11200093-11201275",range.name="LDLR",test = "GRANVIL",maf.cutoff = 0.05,alternative = c("two.sided"),ix.gold = 1,out.digits =4,callrate.cutoff = A Simple Tutorial for Using the rareMETALS0,hwe.range function cutoff =0,max.VT =NULL)
res <- rareMETALS.range(score.stat.file,cov.file,range="19:11200093-11201275",range.name="LDLR",test = "GRANVIL",maf.cutoff = 0.05,alternative = c("two.sided"),ix.gold = 1,out.digits = 4,callrate.cutoff = 0,hwe.cutoff = 0,max.VT = NULL)
gene.name.out p.value.out statistic.out no.site.out beta1.est.out
[1,] "LDLR" "0.6064" "0.2654" "25" "-0.01729"
pos.ref.alt.out \
\
 
[1,] "19:11200093/T/C,19:11200213/G/A,19:11200235/G/A,19:11200272/C/A,19:11200282/G/A,19:11200309/C/A,19:11200412/C/T,19:11200419/C/T,19:11200431/C/T,19:1120\
0442/G/A,19:11200475/C/G,19:11200508/G/A,19:11200514/C/T,19:11200557/G/A,19:11200579/C/T,19:11200728/C/T,19:11200753/T/C,19:11200754/G/A,19:11200806/C/T,19:1\
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