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| * Estimate measures of genetic effect heterogeneities between studies | | * Estimate measures of genetic effect heterogeneities between studies |
| | | |
− | == Exemplar Dataset | + | == 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 | | Four datasets are useful to get you started on how to use rareMETALS R package for meta-analyses of gene-level association test |
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| If you use RVTESTS, your command should be | | If you use RVTESTS, your command should be |
| | | |
− | :bgzip study1.MetaScore.assoc
| + | 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.MetaScore.assoc.gz |
| | | |
− | :tabix -s 1 -b 2 -e 2 -S 1 study1.MetaCov.assoc.gz
| + | tabix -s 1 -b 2 -e 2 -S 1 study1.MetaCov.assoc.gz |
| | | |
| == A Simple Tutorial for Using the rareMETALS.single function == | | == A Simple Tutorial for Using the rareMETALS.single function == |
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| Example: | | Example: |
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− | cov.file <- c("study1.MetaCov.assoc.gz","study2.MetaCov.assoc.gz"); | + | 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")
| + | == A Simple Tutorial for Using the rareMETALS.range function == |
− | | |
− | 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 == | + | 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) |
| | | |
− | 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 | | gene.name.out p.value.out statistic.out no.site.out beta1.est.out |
| [1,] "LDLR" "0.6064" "0.2654" "25" "-0.01729" | | [1,] "LDLR" "0.6064" "0.2654" "25" "-0.01729" |
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| pos.ref.alt.out \ | | 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\ | | [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\ | | 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\ |