RnBeads (version 1.4.0)

mergeSamples,RnBSet-method: mergeSamples

Description

Take an RnBSet object and merge methylation and phenotype information given a grouping column in the pheno table coverage is combined by taking the sum of coverages pheno is combined by concatenating entries from all samples

Usage

"mergeSamples"(object, grp.col)

Arguments

object

input RnBSet object

grp.col

a column name (string) of pheno(rnb.set) that contains unique identifiers for sample groups/replicates to be combined

Value

the modified RnBSet object

Details

combines phenotype information, coverage information and methylation information methylation is combined by taking the average. Detection p-values are combined using Fisher's method. For methylation arrays, bead counts are currently not taken into account. objects of class RnBeadRawSet are automatically converted to RnBeadSet.

Examples

library(RnBeads.hg19)
data(small.example.object)
rnb.set.example
rnb.set.merged <- mergeSamples(rnb.set.example,"Cell_Line")
rnb.set.merged
pheno(rnb.set.merged)