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 1.12.5 Index]