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
htmloutput Produce an html summary report
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"