Quality assessment and low-level analysis for Illumina BeadArray data


[Up] [Top]

Documentation for package ‘beadarray’ version 2.2.0

Help Pages

beadarray-package The beadarray package: a tool for low-level analysis of Illumina BeadArrays
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 Class "beadLevelData"
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
checkPlatform Determine expression chip annotation
checkRegistration Perform check for misregistered array segments.
combine-method Combine two objects.
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 Retrieve the dimensions of an object
ExpressionControlData Control annotation for Illumina expression chips
expressionQCPipeline Flexible bead-level QC pipeline
ExpressionSetIllumina-class Class "ExpressionSetIllumina"
exprs-method 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
illuminaBackground Image processing functions
illuminaChannel-class Class "illuminaChannel"
illuminaForeground Image processing functions
illuminaOutlierMethod Identifier outliers on an array section
illuminaSharpen Image processing functions
imageplot imageplot for beadLevelData object
insertBeadData Add, modify or remove 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
medianBackground Image processing functions
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"
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
processSwathData Prepare iScan data for use with beadarray
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.
removeBeadData Add, modify or remove data in a beadLevelData object
se.exprs-method 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 Display object summary
showArrayMask Show Array Mask
summarize Create a summarized object
[-method Class "ExpressionSetIllumina"
[[-method Class "beadLevelData"