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library(rareMETALS2)
library(rareMETALS2)
res <- rareMETALS2.single(score.stat.file,range="19:42906914-45854919",alternative="two.sided",ix.gold=1,callrate.cutoff=0,hwe.cutoff=0)
res <- rareMETALS2.single(score.stat.file,range="19:42906914-45854919",alternative="two.sided",ix.gold=1,callrate.cutoff=0,hwe.cutoff=0)
###result can be explored as below###
###result can be explored as below###
> names(res)
> names(res)
[1] "p.value" "ref" "alt"
[4] "integratedData" "raw.data" "clean.data"
[7] "statistic" "direction.by.study" "anno"
[10] "af" "afCase" "afCtrl"
[10] "af" "afCase" "afCtrl"
[13] "QC.by.study" "no.sample" "no.case"
[13] "QC.by.study" "no.sample" "no.case"
[16] "no.ctrl" "beta1.est" "beta1.sd"
[16] "no.ctrl" "beta1.est" "beta1.sd"
[19] "hsq.est" "nearby" "pos"
[19] "hsq.est" "nearby" "pos"
> print(res$pos) ###the first 25 position###
> print(res$pos) ###the first 25 position###
[1] "19:42906914" "19:42907064" "19:42907171" "19:42909626" "19:42909645"
[1] "19:42906914" "19:42907064" "19:42907171" "19:42909626" "19:42909645"
[6] "19:42910407" "19:42910445" "19:42910454" "19:42911617" "19:42911769"
[6] "19:42910407" "19:42910445" "19:42910454" "19:42911617" "19:42911769"
