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| 19:43420408/G/C,19:43420415/G/A,19:43420565/C/T,19:43433773/C/T,19:43439628/A/G, | | 19:43420408/G/C,19:43420415/G/A,19:43420565/C/T,19:43433773/C/T,19:43439628/A/G, |
| | | |
| + | '''Function Detail:''' |
| rareMETALS2.range <- function(score.stat.file,cov.file,range,range.name,test='GRANVIL',maf.cutoff=1,alternative=c('two.sided','greater','less'), | | rareMETALS2.range <- function(score.stat.file,cov.file,range,range.name,test='GRANVIL',maf.cutoff=1,alternative=c('two.sided','greater','less'), |
| ix.gold=1,out.digits=4,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0,max.VT=NULL) | | ix.gold=1,out.digits=4,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0,max.VT=NULL) |
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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) |