sesamize {sesame} | R Documentation

## "fix" an RGChannelSet (for which IDATs may be unavailable) with Sesame The input is an RGSet and the output is a sesamized minfi::GenomicRatioSet

### Description

`HDF5Array` package required.

### Usage

    sesamize(
      rgSet,
      naFrac = 1,
      BPPARAM = SerialParam(),
      HDF5 = NULL,
      HDF5SEdestination = paste0(tempdir(check = TRUE), "/sesamize_HDF5_scratch"),
      replace = FALSE
    )

### Arguments

`rgSet` | an RGChannelSet, perhaps with colData of various flavors
`naFrac` | maximum NA fraction for a probe before it gets dropped (1)
`BPPARAM` | get parallel with MulticoreParam(n)
`HDF5` | is the rgSet HDF5-backed? if so, avoid eating RAM (perhaps)
`HDF5SEdestination` | character(1) path to where the HDF5-backed GenomicRatioSet will be stored
`replace` | logical(1) passed to saveHDF5SummarizedExperiment

### Value

a sesamized GenomicRatioSet

### Note

We employ BPREDO for a second chance if bplapply hits an error.

### Examples

    if(FALSE) {
        library(FlowSorted.CordBloodNorway.450k)
        sesamize(FlowSorted.CordBloodNorway.450k[,1:2],
            BPPARAM=MulticoreParam(2))
    }

[Package sesame version 1.12.9 Index]