sesamize: "fix" an RGChannelSet (for which IDATs may be unavailable)...

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

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

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.

sesame documentation built on Nov. 15, 2020, 2:08 a.m.