combine,RnBSet,RnBSet-method {RnBeads} | R Documentation |
Combine two objects inheriting from RnBSet
class
## S4 method for signature 'RnBSet,RnBSet' combine(x, y, type = "all")
x, y |
|
type |
|
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.
combined RnBeadSet
, RnBeadRawSet
or
RnBiseqSet
object
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))