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RareMETALS2 (view source)

Revision as of 15:11, 29 June 2015

4,969 bytes added ,  15:11, 29 June 2015
→‎Conditional Meta-analysis
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== Exemplar Datasets ==
 
== Exemplar Datasets ==
   −
The following exemplar datasets can be downloaded and tested with rareMETALS2 package.
+
The following exemplar datasets [[Media:ExampleDataaset.zip | ExampleDataset.zip]] can be downloaded and tested with rareMETALS2 package.
 
* ''Score Statistics File''
 
* ''Score Statistics File''
−
  [[example1.MetaScore.assoc.gz | example1.MetaScore.assoc.gz]].
  −
  [[example2.MetaScore.assoc.gz | example2.MetaScore.assoc.gz]].
   
* ''Covariance Matrix File''
 
* ''Covariance Matrix File''
−
  [[example1.MetaCov.assoc.gz | example1.MetaCov.assoc.gz]].
+
* ''Tabix index file''
−
  [[example2.MetaCov.assoc.gz | example2.MetaCov.assoc.gz]].  
+
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                                                                                                           
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== 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)
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== 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)
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