Quality assessment and low-level analysis for Illumina BeadArray data


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Documentation for package ‘beadarray’ version 2.0.6

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arrayNames Deprecated Functions
arrayNames-method Class "BeadLevelList"
backgroundCorrectSingleSection Background correct an array-section
BASH BASH - BeadArray Subversion of Harshlight
BASHCompact BASH - Compact Defect Analysis
BASHDiffuse BASH - Diffuse Defect Analysis
BASHExtended BASH - Extended Defect Analysis
beadarrayUsersGuide View beadarray User's Guide
beadLevelData Class "beadLevelData"
beadLevelData-class Class "beadLevelData"
BeadLevelList Class "BeadLevelList"
BeadLevelList-class Class "BeadLevelList"
beadStatusVector Classify each bead according to its control status
BLData beadLevelData object from an example experiment
boxplot-method Class "beadLevelData"
BSData ExpressionSetIllumina object for the example experiment
calculateDetection Calculate detection scores
calculateOutlierStats Outlier distribution stats
checkRegistration Perform check for misregistered array segments.
combine-method Class "ExpressionSetIllumina"
combine-method Class "beadLevelData"
controlProbeDetection Percentage of beads detected
controlProfile Control annotation for Illumina expression chips
convertBeadLevelList Convert a BeadLevelList object into a beadLevelData object
createBeadSummaryData Deprecated Functions
createTargetsFile A function to generate a targets file given a directory of Illumina bead-level files
Detection Class "ExpressionSetIllumina"
Detection-method Class "ExpressionSetIllumina"
Detection<- Class "ExpressionSetIllumina"
Detection<--method Class "ExpressionSetIllumina"
dim-method Class "ExpressionSetIllumina"
dim-method Class "beadLevelData"
ExpressionControlData Control annotation for Illumina expression chips
expressionQCPipeline Flexible bead-level QC pipeline
ExpressionSetIllumina-class Class "ExpressionSetIllumina"
exprs-method Class "ExpressionSetIllumina"
exprs<- Class "ExpressionSetIllumina"
exprs<--method Class "ExpressionSetIllumina"
generateNeighbours Generate matrix of neighbouring beads
genericBeadIntensityPlot Plotting the intensities of selected beads on a section
getAnnotation Storage of annotation information
getArrayData Deprecated Functions
getArrayData-method Class "BeadLevelList"
getBeadData Get raw data from a beadLevelData object
greenChannelTransform Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
HULK HULK - Bead Array Normalization by NEighbourhood Residuals
illuminaChannel-class Class "illuminaChannel"
illuminaOutlierMethod Identifier outliers on an array section
imageplot imageplot for beadLevelData object
insertBeadData Add or modify data in a beadLevelData object
insertSectionData Modify the sectionData slot
logGreenChannelTransform Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
logRatioTransform Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
logRedChannelTransform Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
makeQCTable Tabulate QC scores
medianNormalise Median normalise data in a matrix
nObservations Class "ExpressionSetIllumina"
nObservations-method Class "ExpressionSetIllumina"
nObservations<- Class "ExpressionSetIllumina"
nObservations<--method Class "ExpressionSetIllumina"
normaliseIllumina Normalise Illumina expression data
numBeads Gets the number of beads from a beadLevelData object
numBeads-method Class "beadLevelData"
openTIFF Read the Illumina tiff images
outlierplot Plot outlier locations
plotBeadIntensities Plotting the intensities of selected beads on a section
plotBeadLocations Plot bead locations
plotChipLayout Function to Plot the Layout of an Illumina BeadChip
plotMA Scatter plots and MA-plots for all specified arrays
plotMAXY Scatter plots and MA-plots for all specified arrays
plotTIFF Produce plots of the Illumina tiff images
plotXY Scatter plots and MA-plots for all specified arrays
poscontPlot Plot the positive controls
qcData Class "ExpressionSetIllumina"
qcData-method Class "ExpressionSetIllumina"
quickSummary Create summary values for specified IDs
readBeadSummaryData Read BeadStudio gene expression output
readIllumina Read bead-level Illumina data
readLocsFile Read ".locs" file.
readTIFF Read the Illumina tiff images
redChannelTransform Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
se.exprs-method Class "ExpressionSetIllumina"
se.exprs<- Class "ExpressionSetIllumina"
se.exprs<--method Class "ExpressionSetIllumina"
sectionNames Gets the section names from a beadLevelData Object
sectionNames-method Class "beadLevelData"
setAnnotation Storage of annotation information
setWeights Set weights from BASH
show-method Class "ExpressionSetIllumina"
show-method Class "beadLevelData"
showArrayMask Show Array Mask
summarize Create a summarized object
[-method Class "ExpressionSetIllumina"
[[-method Class "beadLevelData"