SampleSet-class: S4 class object SampleSet

In GreenwoodLab/funtooNorm: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit

S4 class object SampleSet

Description

SampleSet is an S4 class defined for the purpose of running the funtooNorm algorithm. They are lists containing signal data and different variables useful for funtooNorm. The data is separated into the 3 probes types, each having 2 channels (methylated and unmethylated ie : A and B) We then define then the 6 (2*3) labels: AIGrn BIGrn AIRed BIRed AII BII

Value

a S4 object of class SampleSet

Slots

type

Character: is 'minfi' or 'GenomeStudio'

sampleNames

character vector: contain the list of sample names in order used

sampleSize

numeric: the number of samples

nPos

numeric: the number of positions in the ILLUMINA chip

annotation

character: the annotation object from minfi package

cell_type

factor: vector of the cell type for each sample as factors

qntllist

numeric: vector of ordered quantiles

quantiles

list: list of 6 quantiles tables for the 6 signal types

ctl.covmat

matrix: covariance matrix for the model fit

signal

list: list of the values for all 6 probe types.

names

list: list of probes for each type

predmat

list: list of the normalized values for all 6 probe types.

Examples

showClass("SampleSet")

GreenwoodLab/funtooNorm documentation built on April 5, 2022, 3:22 p.m.