anno.merge: Merges multiple annotatedSNPset objects

In sbstatgen/GKnowMTest: Genomic Knowledge-guided Multiple Testing

Description

Function to merge multiple annotatedSNPset objects into a single object.

Usage

anno.merge(anno.list)

Arguments

anno.list

A list of multiple annotatedSNPset objects.

Details

If several objects merged as a single object then all equivalence classes of input objects are merged to form a new equivalence class. eq.map matrix stores this mapping information i.e which input equivalence classes form the new equivalence classes. For a merged object,snp.eq is created by using this new equivalence class. The eq.mat lists are concatenated to hold one binary matrix from each merged object.

Value

It returns an object of annotatedSNPset-class.See annotatedSNPset-class for details.

See Also

anno.create

Examples

## Not run: 
  snpfile <- system.file("sampleData", "snpData.rda", package="GKnowMTest")
  pathfile <- system.file("sampleData", "pathData.rda", package="GKnowMTest")
  anmfile <- system.file("sampleData", "anmData.rda", package="GKnowMTest")

  load(snpfile) ## loads snpdf
  load(pathfile) ## loads a R list of gene symbols
  load(anmfile) ##loads annotation matrix

  snp<-rownames(snpdf)
  ob1=anno.create(snp,path.def=pathlist) ## Genelist as Pathlist

  ##creation of annotation matrix
  res=create.anno.mat(snp,base.path="/home/Datasets/Encode/",
      fl.suffix=".annot.wdist.wcoding")
  anm=res[[1]]

  ob2<-anno.create(snp,anno.mat=anm) #annotation matrix as pathlist
 
## End(Not run)

obfile <- system.file("sampleData", "obData.rda", package="GKnowMTest")
load(obfile) ##loads two mapping objects ob1 and ob2.
ob3=anno.merge(list(ob1,ob2)) 
ob3

sbstatgen/GKnowMTest documentation built on May 27, 2019, 7:40 a.m.