openSesame {sesame} | R Documentation

## The openSesame pipeline

### Description

This function is a simple wrapper of noob + nonlinear dye bias correction + pOOBAH masking.

### Usage

    openSesame(
      x,
      platform = "",
      manifest = NULL,
      what = "beta",
      BPPARAM = SerialParam(),
      ...
    )

### Arguments

`x` | SigSet(s), IDAT prefix(es), minfi GenomicRatioSet(s), or RGChannelSet(s)
`platform` | optional platform string
`manifest` | optional dynamic manifest
`what` | either 'sigset' or 'beta'
`BPPARAM` | get parallel with MulticoreParam(n)
`...` | parameters to getBetas

### Details

If the input is an IDAT prefix or a `SigSet`, the output is the beta value numerics. If the input is a minfi GenomicRatioSet or RGChannelSet, the output is the sesamized GenomicRatioSet.

### Value

a numeric vector for processed beta values

### Examples

    sset <- sesameDataGet('HM450.1.TCGA.PAAD')$sset
    IDATprefixes <- searchIDATprefixes(
        system.file("extdata", "", package = "sesameData"))
    betas <- openSesame(IDATprefixes)

[Package sesame version 1.6.0 Index]