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 1.12.1 Index]