openSesame {sesame}R Documentation

The openSesame pipeline

Description

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

Usage

openSesame(x, platform = "", manifest = NULL, BPPARAM = SerialParam(), ...)

Arguments

x

SigDF(s), IDAT prefix(es), minfi GenomicRatioSet(s), or RGChannelSet(s)

platform

optional platform string

manifest

optional dynamic manifest

BPPARAM

get parallel with MulticoreParam(n)

...

parameters to getBetas

Details

If the input is an IDAT prefix or a SigDF, 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

sdf <- sesameDataGet('HM450.1.TCGA.PAAD')$sdf
IDATprefixes <- searchIDATprefixes(
    system.file("extdata", "", package = "sesameData"))
betas <- openSesame(IDATprefixes)

[Package sesame version 1.12.5 Index]