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I have created a '''google group''' for discussion on the usage and for bug reports etc. If you find any issues to the package and think that the discussions may also benefit others, please post them to the user group. Here is the link to the discussion group https://groups.google.com/forum/#!forum/raremetals
I have created a '''google group''' for discussion on the usage and for bug reports etc. If you find any issues to the package and think that the discussions may also benefit others, please post them to the user group. Here is the link to the discussion group https://groups.google.com/forum/#!forum/raremetals
== Exemplar Datasets ==
The following exemplar datasets [[Media:ExampleDataaset.zip | ExampleDataset.zip]] can be downloaded and tested with rareMETALS2 package.
* ''Score Statistics File''
* ''Covariance Matrix File''
* ''Tabix index file''
These files are all automatically generated by rvtests.
== Meta-analysis of Single Variant Associations ==
== Meta-analysis of Single Variant Associations ==
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)
'''A Simple Tutorial for Using the rareMETALS2.single function'''
'''Example:'''
Use the ExampleDataset above which is a set of single variant score statistics and their covariance matrices.
cov.file <- c("example1.MetaCov.assoc.gz","example2.MetaCov.assoc.gz")
score.stat.file <- c("example1.MetaScore.assoc.gz","example2.MetaScore.assoc.gz")
library(rareMETALS2)
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)
'''Relevant Parameters''':
'''Relevant Parameters''':
* '''score.stat.file''' files of score statistics
* '''score.stat.file''' files of score statistics
== 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)
