openSesame: The openSesame pipeline

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

The openSesame pipeline

Description

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

Usage

openSesame(
  x,
  prep = "QCDPB",
  prep_args = NULL,
  manifest = NULL,
  func = getBetas,
  BPPARAM = SerialParam(),
  platform = "",
  min_beads = 1,
  ...
)

Arguments

x	SigDF(s), IDAT prefix(es)
prep	preprocessing code, see ?prepSesame
prep_args	optional preprocessing argument list, see ?prepSesame
manifest	optional dynamic manifest
func	either getBetas or getAFs, if NULL, then return SigDF list
BPPARAM	get parallel with MulticoreParam(n)
platform	optional platform string
min_beads	minimum bead number, probes with R or G smaller than this threshold will be masked. If NULL, no filtering based on bead count will be applied. Default to 1.
...	parameters to getBetas

Details

Please use mask=FALSE to turn off masking.

If the input is an IDAT prefix or a SigDF, the output is the beta value numerics.

Value

a numeric vector for processed beta values

Examples

in_dir <- system.file("extdata", "", package = "sesameData")
betas <- openSesame(in_dir)
## or
IDATprefixes <- searchIDATprefixes(in_dir)
betas <- openSesame(IDATprefixes)

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.