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Last data update: 2014.03.03

R: Class LumiBatch: contain and describe Illumina microarray...

LumiBatch-class

R Documentation

Class LumiBatch: contain and describe Illumina microarray data

Description

This is a class representation for Illumina microarray data. It extends ExpressionSet.

Extends

Directly extends class ExpressionSet.

Creating Objects

new("LumiBatch", exprs = [matrix], se.exprs = [matrix], beadNum = [matrix], detection = [matrix], phenoData = [AnnotatedDataFrame], history = [data.frame], ...)

LumiBatch instances are usually created through new("LumiBatch", ...). The arguments to new should include exprs and se.exprs, others can be missing, in which case they are assigned default values.

Objects can be created using the function lumiR.

Slots

Slot specific to LumiBatch:

history:: a data.frame recording the operation history of the LumiBatch object.
controlData:: a data.frame with first two columns as "controlType" and "ProbeID". The rest columns are the control probe expression amplitudes for individual samples.
QC:: a the quality control information of the LumiBatch object, returned by lumiQ function.

Slots inherited from ExpressionSet:

assayData: contains equal dimensional matrices: exprs (contains gene expression level, which is the mean of its bead replicates.), se.exprs (contains gene expression standard error, which is the standard error of its bead replicates.), beadNum (records the number of beads for the probe.), detection (records the detection p-value of the probe. The number is from [0,1]. By default, < 0.01 indicates good detection.). For more details of assayData, please see ExpressionSet
phenoData:: See eSet
experimentData:: See eSet
annotation:: See eSet

Methods

Class-specific methods:

se.exprs(LumiBatch), se.exprs(LumiBatch,matrix)<-:: Access and set elements named se.exprs in the AssayData-class slot.
beadNum(LumiBatch), beadNum(LumiBatch)<-:: Access and set elements named beadNum in the AssayData-class slot. Use "beadNum(LumiBatch) <- NULL" to remove the beadNum element.
detection(LumiBatch), detection(LumiBatch)<-:: Access and set elements named detection in the AssayData-class slot. Use "detection(LumiBatch) <- NULL" to remove the detection element.
getHistory(LumiBatch):: Access the operation history of LumiBatch object.

Derived from ExpressionSet (For the directly inherited methods, please see ExpressionSet and eSet):

combine(LumiBatch,missing):: Combine two LumiBatch objects, including history slot. See eSet
exprs(LumiBatch), exprs(LumiBatch,matrix)<-:: Access and set elements named exprs in the AssayData-class slot.
object[(i,j):: Conduct subsetting of the data in a LumiBatch object

Standard generic methods (For the directly inherited methods, please see ExpressionSet and eSet):

initialize(LumiBatch):: Object instantiation, used by new; not to be called directly by the user.
validObject(LumiBatch):: Validity-checking method, ensuring that exprs and se.exprs is a member of assayData. Other validity check is the same as checkValidity(ExpressionSet).
show(LumiBatch): A summary of the LumiBatch object.

Author(s)

Pan Du, Simon Lin

Examples

## load example data
data(example.lumi)

## show the summary of the data
# summary(example.lumi)
example.lumi	

## get expression matrix
temp <- exprs(example.lumi)

## get a subset
temp <- example.lumi[,1]	## retrieve the first sample

## get the probe id
featureNames(example.lumi)[1:3]

## combine LumiBatch objects
temp <- combine(example.lumi[,1], example.lumi[,3])
temp

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(lumi)
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/LumiBatch-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LumiBatch-class
> ### Title: Class LumiBatch: contain and describe Illumina microarray data
> ### Aliases: class:LumiBatch LumiBatch-class LumiBatch se.exprs se.exprs<-
> ###   se.exprs,ExpressionSet-method se.exprs<-,ExpressionSet-method
> ###   se.exprs<-,ExpressionSet,ANY-method beadNum beadNum<-
> ###   beadNum,ExpressionSet-method beadNum<-,ExpressionSet-method
> ###   beadNum<-,ExpressionSet,ANY-method detection detection<-
> ###   detection,ExpressionSet-method detection<-,ExpressionSet-method
> ###   detection<-,ExpressionSet,ANY-method controlData controlData<-
> ###   controlData,LumiBatch-method controlData<-,LumiBatch-method
> ###   controlData<-,LumiBatch,ANY-method initialize,LumiBatch-method
> ###   summary,LumiBatch-method show,LumiBatch-method
> ###   combine,LumiBatch,LumiBatch-method
> ###   combine,ExpressionSet,LumiBatch-method
> ###   combine,LumiBatch,ExpressionSet-method [,LumiBatch-method
> ###   [,LumiBatch,ANY,ANY,ANY-method sampleNames<-,LumiBatch,ANY-method
> ###   getHistory,LumiBatch-method getHistory
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## load example data
> data(example.lumi)
> 
> ## show the summary of the data
> # summary(example.lumi)
> example.lumi	
Summary of data information:
Illumina Inc. BeadStudio version 1.4.0.1
		Normalization = none
		Array Content = 11188230_100CP_MAGE-ML.XML
		Error Model = none
		DateTime = 2/3/2005 3:21 PM
		Local Settings = en-US
		

Major Operation History:
            submitted            finished
1 2007-04-22 00:08:36 2007-04-22 00:10:36
2 2007-04-22 00:10:36 2007-04-22 00:10:38
3 2007-04-22 00:13:06 2007-04-22 00:13:10
4 2007-04-22 00:59:20 2007-04-22 00:59:36
                                             command lumiVersion
1           lumiR("../data/Barnes_gene_profile.txt")       1.1.6
2                             lumiQ(x.lumi = x.lumi)       1.1.6
3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1")       1.1.6
4            Subsetting 8000 features and 4 samples.       1.1.6

Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 8000 features, 4 samples 
  element names: beadNum, detection, exprs, se.exprs 
protocolData: none
phenoData
  sampleNames: A01 A02 B01 B02
  varLabels: sampleID label
  varMetadata: labelDescription
featureData
  featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ...
    33KnLHy.RFaieogAF4 (8000 total)
  fvarLabels: TargetID
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: lumiHumanAll.db 
Control Data: Available
QC information: Please run summary(x, 'QC') for details!
> 
> ## get expression matrix
> temp <- exprs(example.lumi)
> 
> ## get a subset
> temp <- example.lumi[,1]	## retrieve the first sample
> 
> ## get the probe id
> featureNames(example.lumi)[1:3]
[1] "oZsQEQXp9ccVIlwoQo" "9qedFRd_5Cul.ueZeQ" "N5YrunuK0q.yIkukis"
> 
> ## combine LumiBatch objects
> temp <- combine(example.lumi[,1], example.lumi[,3])
The sample names in the controlData don't match sampleNames(object).
> temp
Summary of data information:
Illumina Inc. BeadStudio version 1.4.0.1
		Normalization = none
		Array Content = 11188230_100CP_MAGE-ML.XML
		Error Model = none
		DateTime = 2/3/2005 3:21 PM
		Local Settings = en-US
		

Major Operation History:
            submitted            finished
1 2007-04-22 00:08:36 2007-04-22 00:10:36
2 2007-04-22 00:10:36 2007-04-22 00:10:38
                                   command lumiVersion
1 lumiR("../data/Barnes_gene_profile.txt")       1.1.6
2                   lumiQ(x.lumi = x.lumi)       1.1.6
...
             submitted            finished
12 2016-07-06 21:25:13 2016-07-06 21:25:13
13 2016-07-06 21:25:13 2016-07-06 21:25:13
                                                 command lumiVersion
12                             Subsetting 8000 features.      2.24.0
13 combine(x = example.lumi[, 1], y = example.lumi[, 3])      2.24.0

Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 8000 features, 2 samples 
  element names: beadNum, detection, exprs, se.exprs 
protocolData: none
phenoData
  sampleNames: A01 B01
  varLabels: sampleID label
  varMetadata: labelDescription
featureData
  featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ...
    33KnLHy.RFaieogAF4 (8000 total)
  fvarLabels: TargetID
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: lumiHumanAll.db 
Control Data: Available
QC information: Please run summary(x, 'QC') for details!
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>