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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###
> names(res)
[1] "p.value" "ref" "alt"
[4] "integratedData" "raw.data" "clean.data"
[7] "statistic" "direction.by.study" "anno"
[10] "af" "afCase" "afCtrl"
[13] "QC.by.study" "no.sample" "no.case"
[16] "no.ctrl" "beta1.est" "beta1.sd"
[19] "hsq.est" "nearby" "pos"
> print(res$pos) ###the first 25 position###
[1] "19:42906914" "19:42907064" "19:42907171" "19:42909626" "19:42909645"
[6] "19:42910407" "19:42910445" "19:42910454" "19:42911617" "19:42911769"
[11] "19:42911869" "19:42911877" "19:42912216" "19:42912223" "19:42912229"
[16] "19:42912244" "19:42912441" "19:42914568" "19:42914587" "19:42914626"
[21] "19:42914665" "19:42914668" "19:42914682" "19:42914703" "19:42914772"
> print(res$p.value) ###the P-value of the first 25 position###
[1] NA 0.311755625 NA 0.793836855 0.292744822 0.393802545
[7] NA 0.175761040 0.106303677 NA 0.217054457 NA
[13] 0.063036490 0.516061931 0.089290910 NA NA NA
[19] NA 0.364595966 NA 0.482571300 NA 0.434685495
[25] NA
'''Function Detail:'''
rareMETALS2.single <- function(score.stat.file,range,alternative=c('two.sided','greater','less'),ix.gold=1,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0)
rareMETALS2.single <- function(score.stat.file,range,alternative=c('two.sided','greater','less'),ix.gold=1,callrate.cutoff=0,hwe.cutoff=0,hwe.ctrl.cutoff=0)
'''Relevant Parameters''':
'''Relevant Parameters''':
