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RareMETALS (view source)

Revision as of 22:16, 24 March 2015

33 bytes added ,  22:16, 24 March 2015
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* Estimate measures of genetic effect heterogeneities between studies  
 
* Estimate measures of genetic effect heterogeneities between studies  
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== Exemplar Dataset
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== 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
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:bgzip study1.MetaScore.assoc
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  bgzip study1.MetaScore.assoc
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:tabix -s 1 -b 2 -e 2 -S 1 study1.MetaScore.assoc.gz
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  tabix -s 1 -b 2 -e 2 -S 1 study1.MetaScore.assoc.gz
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:tabix -s 1 -b 2 -e 2 -S 1 study1.MetaCov.assoc.gz
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  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");
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  library(rareMETALS)
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  cov.file <- c("study1.MetaCov.assoc.gz","study2.MetaCov.assoc.gz");
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  score.stat.file <- c("study1.MetaScore.assoc.gz","study2.MetaScore.assoc.gz")
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  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);
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score.stat.file <- c("study1.MetaScore.assoc.gz","study2.MetaScore.assoc.gz")
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== A Simple Tutorial for Using the rareMETALS.range function ==
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  −
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 ==
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  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)
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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\
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