QC, normalisation, annotation and exploration of Illumina BeadChip data

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Documentation for package `BeadExplorer' version 1.2.0

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addManifest Add annotation data
annotation,beadQC-method Class "beadQC"
annotation<-,beadQC,ANY-method Class "beadQC"
annotation<-,beadQC-method Class "beadQC"
batchAnalysis Batch Analysis
beadAnalysis Automated Bead Analysis
beadData-class Class "beadData"
beadQC-class Class "beadQC"
boxplot,beadData-method Class "beadData"
boxplotArrays Plot a series of QC boxplots
boxplotQC Plot a subset of QC boxplots
clusterplot Plots a hierarchical cluster plot
cutoff Determine the number of transcripts that pass a fold change cut-off criteria
detectionCalls Get percentage of genes called present
detectionCalls,beadData-method Class "beadData"
detExprs Accessor Methods for beadData class
detExprs,beadData-method Class "beadData"
dotplotArrays Plots a series of dotplots for BeadChip QC data
dotplotQC Plot a subset of QC dotplots
examplebeadData An example of a beadData object
examplebeadQC An example of a beadQC object
extract Extract columns from a BeadStudio file
fileOrigin Accessor Methods for beadData class
fileOrigin,beadData-method Class "beadData"
fileOrigin,beadQC-method Class "beadQC"
filterData Filter data based on detection score
getAnnot Get annotation information
getArrayStats Get QC values for a BeadChip
getDet Get detection scores for a given gene(s)
getExprs Get expression intensities for a given gene(s)
getID Get expression data for a given gene ID
getQC Generate QC data
getQC2 Generate QC data
htmloutput Produce an html summary report
HumRef8 A mapping file of Illumina Probe IDs to control type
HumWG6 A mapping file of Illumina Probe IDs to control type
multiDensity Plot multiple density functions
multiecdf Plot multiple estimated cumulative density function graphs
nGenes Accessor Methods for beadData class
nGenes,beadData-method Class "beadData"
normalise Normalise a beadData object
normMethod Accessor Methods for beadData class
normMethod,beadData-method Class "beadData"
nSamples Accessor Methods for beadData class
nSamples,beadData-method Class "beadData"
pairs,beadData-method Class "beadData"
param Accessor Methods for beadData class
param,beadData-method Class "beadData"
pc Principal component plot
plot,beadData,missing-method Class "beadData"
plotSamples QC sample plots
readBead Read BeadStudio expression data file
readManifest Read annotation data
readQC Reads log file data
sampleQC Accessor Methods for beadData class
sampleQC,beadQC-method Class "beadQC"
scatterPlot Pairwise scattergraph of data
signalMeans Accessor Methods for beadData class
signalMeans,beadData-method Class "beadData"
summary,beadData-method Class "beadData"
write.beadData Write beadData to a file
writeQC Writes QC data to a log file
[,beadData-method Class "beadData"
[,beadQC-method Class "beadQC"