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[19] NA 0.364595966 NA 0.482571300 NA 0.434685495
[19] NA 0.364595966 NA 0.482571300 NA 0.434685495
[25] NA
[25] NA
'''Function Detail:'''
'''Function Detail:'''
== Meta-analysis of Gene-level Association ==
== Meta-analysis of Gene-level Association ==
'''A Simple Tutorial for Using the rareMETALS2.range function'''
'''Example''':
res1 <- rareMETALS2.range(score.stat.file,cov.file,range="19:42906914-45854919",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)
> print(res1$res.out)
gene.name.out p.value.out statistic.out no.site.out beta1.est.out
[1,] "LDLR" "0.5575" "0.344" "332" "-0.01899"
beta1.sd.out maf.cutoff.out direction.burden.by.study.out
[1,] "0.03237" "0.05" "+-"
direction.meta.single.var.out
[1,] "++--+++-+--++-++-++---++-++-+----++-+++-++-++--+--++-++----++-++++++++---+++-------+++--++-++---++----++--+--+-+-++--+++++++-++-++--
--+-+++----+++----++---+---+---++++---+-+--+--+++--+--+-++--++-+-+++---+++++-----++--+-++---+----++-+-++--+-+++-++-+++-+--++---+---
+++++-+----+++ -+--++---+---++++---+++---+-+++++----+---+-+----+++-++-"
top.singlevar.pos top.singlevar.refalt top.singlevar.pval top.singlevar.af
[1,] "19:45662295" "G/A" "7.804e-15" "0.02303"
pos.ref.alt.out
[1,] "19:42907064/A/G,19:42909626/C/T,19:42909645/C/T,19:42910407/C/T,19:42910454/C/T,19:42911617/T/C,19:42911869/C/T,19:42912216/C/T,19:42912223/C/T,
19:42912229/C/T,19:42914626/C/T,19:42914668/G/A,19:42914703/C/T,19:42914880/C/T,19:42930652/C/T,19:42930721/G/A,19:42931022/C/T,19:43013329/G/T,19:43031219/T/C,
19:43093001/G/A,19:43093011/C/T,19:43093026/T/C,19:43097692/C/T,19:43097788/C/T,19:43243059/C/T,19:43268142/G/T,19:43411959/C/G,19:43411997/G/A,19:43420322/C/T,
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)
== 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)
