get.table,RnBDiffMeth-method {RnBeads} | R Documentation

## get.table-methods

### Description

Gets a differential methylation table

### Usage

    ## S4 method for signature 'RnBDiffMeth'
    get.table(object, comparison, region.type,
      undump = TRUE, return.data.frame = FALSE)

### Arguments

`object` | `RnBDiffMeth` object
`comparison` | character or index of the comparison of the table to retrieve
`region.type` | character or index of the region type of the table to retrieve
`undump` | Flag indicating whether to convert the table into a matrix instead of using the file descriptor. Only meaningful if the if the objects's `disk.dump` slot is true.
`return.data.frame` | should a data.frame be returned instead of a matrix?

### Value

differential methylation table. See `computeDiffMeth.bin.site` and `computeDiffMeth.bin.region` for details.

### Author(s)

Fabian Mueller

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
    dm.promoters <- get.table(dm,get.comparisons(dm)[1],"promoters",return.data.frame=TRUE)
    summary(dm.promoters)

[Package RnBeads version 1.12.1 Index]