mergeSamples,RnBSet-method {RnBeads}R Documentation

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

## S4 method for signature 'RnBSet'
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

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.

Value

the modified RnBSet object

Note

Requires the packages foreach and doParallel.

Author(s)

Fabian Mueller

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)
[Package RnBeads version 1.10.8 Index]