# QC, normalisation, annotation and exploration of Illumina BeadChip data

## Documentation for package ‘BeadExplorer’ version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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"