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| '''Example''': | | '''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) | | 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$res.out) | + | > print(res1$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, |
| | | |
| 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'), |