SigSet-class: SigSet class

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

This is the main data class for SeSAMe. The class holds different classes of signal intensities.

The function takes a string describing the platform of the data. It can be one of "HM27", "HM450" or "EPIC".

The function takes a string describing the platform of the data. It can be one of "HM27", "HM450" or "EPIC".

Usage

## S4 method for signature 'SigSet'
initialize(.Object, platform, ...)

SigSet(...)

Arguments

.Object	target object
platform	"EPIC", "HM450", "HM27" or other strings for custom arrays
...	additional arguments

Value

a SigSet object

a SigSet object

Slots

IG

intensity table for type I probes in green channel

IR

intensity table for type I probes in red channel

II

intensity table for type II probes

oobG

out-of-band probes in green channel

oobR

out-of-band probes in red channel

ctl

all the control probe intensities

pval

named numeric vector of p-values

extra

extra data, currently, IGG => Type-I green that is inferred to be green IRR => Type-I red that is inferred to be red pvals => list of other pvals

platform

"EPIC", "HM450" or "HM27"

Examples

## Create an empty EPIC object.
SigSet("EPIC")
SigSet('EPIC')

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