combine-methods: combine-methods

In RnBeads: RnBeads

Description

Combine two objects inheriting from RnBSet class

Usage

## S4 method for signature 'RnBSet,RnBSet'
combine(x, y, type = "all")

Arguments

x, y	RnBeadSet, RnBeadRawSet or RnBiseqSet object
type	character singleton defining the set operation applied to the two site sets, one of "all", "all.x", "all.y" or "common"

Details

Combine method supports a merge of any two RnBSet objects that contain data of the same specie. In case a non-synonymous merge is performed, the class conversion will follow the following hierarchy: RnBeadSet < RnBeadRawSet < RnBiseqSet. In case x and y are both array data containers (RnBeadSet or RnBeadRawSet), the resulting object will have an annotation that corresponds to the newer array version (27k < 450k < EPIC). The sample sets of x and y should be unique. Sample annotation information is merged only for columns which have identical names in both objects. CpG sites of the new object are a union of those present in both objects.

Value

combined RnBeadSet, RnBeadRawSet or RnBiseqSet object

Examples

library(RnBeads.hg19)
data(small.example.object)
r1 <- rnb.set.example
r1 <- remove.samples(r1,samples(rnb.set.example)[1:5])
i <- which(r1@sites[,2] == 15 | r1@sites[,2] == 21)
sites.rem.r1 <- union(sample(1:nrow(meth(rnb.set.example)),500),i)
r1 <- remove.sites(r1,sites.rem.r1)
r2 <- rnb.set.example
r2 <- remove.samples(r2,samples(rnb.set.example)[6:12])
sites.rem.r2 <- sample(1:nrow(meth(rnb.set.example)),800)
r2 <- remove.sites(r2,sites.rem.r2)
rc <- combine(r1,r2)
#assertion: check the number of sites
sites.rem.c <- intersect(sites.rem.r1,sites.rem.r2)
(nrow(meth(rnb.set.example))-length(sites.rem.c)) == nrow(meth(rc))

RnBeads documentation built on March 3, 2021, 2 a.m.