131
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→A Simple Tutorial for Using the rareMETALS.range function
res <- rareMETALS.range(score.stat.file,cov.file,range="19:11200093-11201275",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)
res <- rareMETALS.range(score.stat.file,cov.file,range="19:11200093-11201275",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)
A tabular result is stored in res$res.out:
res$res.out
gene.name.out p.value.out statistic.out no.site.out beta1.est.out
[1,] "LDLR" "0.6064" "0.2654" "25" "-0.01729"
beta1.sd.out maf.cutoff.out direction.burden.by.study.out
[1,] "0.03357" "0.05" "--"
direction.meta.single.var.out top.singlevar.pos top.singlevar.refalt
[1,] "---++-+--+-+++++--+++++-+" "19:11200431" "C/T"
top.singlevar.pval top.singlevar.af
[1,] "0.004709" "0.01038"
pos.ref.alt.out \
\
[1,] "19:11200093/T/C,19:11200213/G/A,19:11200235/G/A,19:11200272/C/A,19:11200282/G/A,19:11200309/C/A,19:11200412/C/T,19:11200419/C/T,19:11200431/C/T,19:1120\
0442/G/A,19:11200475/C/G,19:11200508/G/A,19:11200514/C/T,19:11200557/G/A,19:11200579/C/T,19:11200728/C/T,19:11200753/T/C,19:11200754/G/A,19:11200806/C/T,19:1\
1200839/T/A,19:11200840/C/A,19:11200896/C/T,19:11201259/G/C,19:11201274/C/T,19:11201275/A/T"
More detailed results can be found in a list res$res.list
