openSesame: The openSesame pipeline

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

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)

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