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, ...)

Arguments

x

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

...

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)

[Package sesame version 1.0.0 Index]