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== Conditional Meta-analysis ==
== Conditional Meta-analysis ==
'''A Simple Tutorial for Using the conditional.rareMETALS2.single'''
'''Example'''
res2<-conditional.rareMETALS2.single(candidate.variant.vec=c("19:42906914","19:45854819"), score.stat.file, cov.file,known.variant.vec=c("19:43995275","19:44047839","19:44084155"), maf.cutoff=0.05, no.boot =1000,
alternative = c("two.sided"), ix.gold = 1,out.digits = 4, callrate.cutoff = 0, hwe.cutoff = 0,p.value.known.variant.vec = NA, anno.known.variant.vec = NA,anno.candidate.variant.vec = NA)
> print(res2$res.out)
POS REF ALT N:N_CASE:N_CTRL PVALUE AF:AF_CASE:AF_CTRL BETA_EST
[1,] "19:42906914" "G" "T" "4012:2008:2004" "NaN" "0:0:0" "NaN"
[2,] "" "" "" "4012:2008:2004" NA "0:NA:NA" NA
BETA_SD DIRECTION_BY_STUDY ANNO
[1,] "Inf" "==" "N/A"
[2,] NA NA ""
POS_REF_ALT_ANNO_KNOWN
[1,] "0"
[2,] "19:43995275/NA/NA,19:44047839/C/T,19:44084155/NA/NA"
'''Function Detail:'''
conditional.rareMETALS2.single <- function(candidate.variant.vec,score.stat.file,cov.file,known.variant.vec,maf.cutoff,no.boot=10000,alternative=c('two.sided','greater','less'),
conditional.rareMETALS2.single <- function(candidate.variant.vec,score.stat.file,cov.file,known.variant.vec,maf.cutoff,no.boot=10000,alternative=c('two.sided','greater','less'),
ix.gold=1,out.digits=4,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0,p.value.known.variant.vec=NA,anno.known.variant.vec=NA,anno.candidate.variant.vec=NA)
ix.gold=1,out.digits=4,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0,p.value.known.variant.vec=NA,anno.known.variant.vec=NA,anno.candidate.variant.vec=NA)
