Class "MethyLumiQC" for holding Illumina methylation QC data

Description

This class inherits from the MethyLumi class (and therefore, from eSet in Biobase) and is designed to hold QC data from Illumina Beadstudio output. These data can be potentially useful when determining the cause for quality problems.

Objects from the Class

Objects can be created by calls of the form new("MethyLumiQC", assayData, phenoData, featureData, experimentData, annotation, betas).

Slots

assayData:

Object of class "AssayData"

phenoData:

Object of class "AnnotatedDataFrame"

featureData:

Object of class "AnnotatedDataFrame" containing the annotation columns from the Illumina Beadstudio output. In particular, the names of the probes describe the types of control probes.

experimentData:

Object of class "MIAME"

annotation:

Object of class "character", not currently used

.__classVersion__:

Object of class "Versions"

Extends

Class "MethyLumi", directly. Class "eSet", by class "MethyLumi", distance 2. Class "VersionedBiobase", by class "MethyLumi", distance 3. Class "Versioned", by class "MethyLumi", distance 4.

Methods

initialize

signature(.Object = "MethyLumiQC")

Cy3.N

signature(object = "MethyLumiQC"): ...

Cy3<-

signature(object = "MethyLumiQC", value = "matrix"): ...

Cy5.N

signature(object = "MethyLumiQC"): ...

Cy5<-

signature(object = "MethyLumiQC", value = "matrix"): ...

QCdata<-

signature(object = "MethyLumiSet", value = "MethyLumiQC"): ...

combine

signature(x = "MethyLumiQC", y = "MethyLumiQC"): ...

controlData<-

signature(object = "MethyLumiSet", value = "MethyLumiQC"): ...

controlTypes

signature(object = "MethyLumiQC"): determine the character vector of control types from the QCdata information

hist

signature(x = "MethyLumiQC"): ...

intensitiesByChannel

signature(object = "MethyLumiQC"): ...

methylated

signature(object = "MethyLumiQC"): ...

negctls.stderr

signature(object = "MethyLumiQC", channel = "character"): ...

negctls.stderr

signature(object = "MethyLumiQC", channel = "missing"): ...

negctls

signature(object = "MethyLumiQC", channel = "character"): ...

negctls

signature(object = "MethyLumiQC", channel = "missing"): ...

negnorm

signature(object = "MethyLumiQC", channel = "character"): ...

negnorm

signature(object = "MethyLumiQC", channel = "missing"): ...

normctls

signature(object = "MethyLumiQC"): ...

qcplot

signature(object = "MethyLumiQC", what, ...): QC plots of various controltypes

unmethylated

signature(object = "MethyLumiQC"): ...

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

See Also

methylumiR, MethyLumiSet, MethyLumi, eSet

Examples

showClass("MethyLumiQC")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(methylumi)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: scales
Loading required package: reshape2
Loading required package: ggplot2
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: FDb.InfiniumMethylation.hg19
Loading required package: GenomicFeatures
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: org.Hs.eg.db

Loading required package: minfi
Loading required package: lattice
Loading required package: SummarizedExperiment

Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:matrixStats':

    rowRanges

Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methylumi/MethyLumiQC-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MethyLumiQC-class
> ### Title: Class '"MethyLumiQC"' for holding Illumina methylation QC data
> ### Aliases: MethyLumiQC-class Cy3.N,MethyLumiQC-method
> ###   Cy3<-,MethyLumiQC,matrix-method Cy5.N,MethyLumiQC-method
> ###   Cy5<-,MethyLumiQC,matrix-method
> ###   QCdata<-,MethyLumiSet,MethyLumiQC-method
> ###   combine,MethyLumiQC,MethyLumiQC-method
> ###   controlData<-,MethyLumiSet,MethyLumiQC-method
> ###   controlTypes,MethyLumiQC-method hist,MethyLumiQC-method
> ###   intensitiesByChannel,MethyLumiQC-method methylated,MethyLumiQC-method
> ###   negctls.stderr,MethyLumiQC,character-method
> ###   negctls.stderr,MethyLumiQC,missing-method
> ###   negctls,MethyLumiQC,character-method
> ###   negctls,MethyLumiQC,missing-method
> ###   negnorm,MethyLumiQC,character-method
> ###   negnorm,MethyLumiQC,missing-method normctls,MethyLumiQC-method
> ###   qcplot,MethyLumiQC-method unmethylated,MethyLumiQC-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("MethyLumiQC")
Class "MethyLumiQC" [package "methylumi"]

Slots:
                                                               
Name:           assayData          phenoData        featureData
Class:          AssayData AnnotatedDataFrame AnnotatedDataFrame
                                                               
Name:      experimentData         annotation       protocolData
Class:              MIAxE          character AnnotatedDataFrame
                         
Name:   .__classVersion__
Class:           Versions

Extends: 
Class "MethyLumi", directly
Class "QCDataOrNULL", directly
Class "eSet", by class "MethyLumi", distance 2
Class "methylData", by class "MethyLumi", distance 2
Class "VersionedBiobase", by class "MethyLumi", distance 3
Class "Versioned", by class "MethyLumi", distance 4
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>