# Quality assessment and low-level analysis for Illumina BeadArray data

## Documentation for package ‘beadarray’ version 2.28.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G H I L M N O P Q R S W misc

beadarray-package | The beadarray package: a tool for low-level analysis of Illumina BeadArrays

## -- A --

addFeatureData | Add probe data
annotation | Storage of annotation information
annotation-method | Storage of annotation information
annotation<--method | Storage of annotation information
arrayNames | Deprecated Functions
arrayNames-method | Class "BeadLevelList"
ArrayWeights | Class "limmaResults"
ArrayWeights-method | Class "limmaResults"
ArrayWeights<- | Class "limmaResults"
ArrayWeights<--method | Class "limmaResults"

## -- B --

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"
beadRegistrationData-class | Class "beadRegistrationData"
beadStatusVector | Classify each bead according to its control status
boxplot-method | Boxplots from summary data
boxplot-method | Class "beadLevelData"
boxplot-method | Class "beadRegistrationData"

## -- C --

calculateDetection | Calculate detection scores
calculateOutlierStats | Outlier distribution stats
checkPlatform | Deprecated Functions
checkRegistration | Perform check for misregistered array segments.
combine-method | Combine two objects.
combinedControlPlot | Flexible bead-level QC pipeline
ContrastMatrix | Class "limmaResults"
ContrastMatrix-method | Class "limmaResults"
ContrastMatrix<- | Class "limmaResults"
ContrastMatrix<--method | Class "limmaResults"
controlProbeDetection | Percentage of beads detected
convertBeadLevelList | Convert a BeadLevelList object into a beadLevelData object
createBeadSummaryData | Deprecated Functions
createGEOMatrix | Create files for a Gene Expression Omnibus submission
createGEOMeta | Create files for a Gene Expression Omnibus submission
createTargetsFile | A function to generate a targets file given a directory of Illumina bead-level files

## -- D --

DesignMatrix | Class "limmaResults"
DesignMatrix-method | Class "limmaResults"
DesignMatrix<- | Class "limmaResults"
DesignMatrix<--method | Class "limmaResults"
Detection | Class "ExpressionSetIllumina"
Detection-method | Class "ExpressionSetIllumina"
Detection<- | Class "ExpressionSetIllumina"
Detection<--method | Class "ExpressionSetIllumina"
dim-method | Class "limmaResults"
dim-method | Retrieve the dimensions of an object

## -- E --

expressionQCPipeline | Flexible bead-level QC pipeline
ExpressionSetIllumina-class | Class "ExpressionSetIllumina"
exprs-method | Class "ExpressionSetIllumina"
exprs<--method | Class "ExpressionSetIllumina"

## -- G --

generateNeighbours | Generate matrix of neighbouring beads
genericBeadIntensityPlot | Plotting the intensities of selected beads on a section
getAnnotation | Deprecated Functions
getArrayData | Deprecated Functions
getArrayData-method | Class "BeadLevelList"
getBeadData | Get raw data from a beadLevelData object
getControlProfile | Storage of annotation information
greenChannel | Class "illuminaChannel"
greenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.

## -- H --

HULK | HULK - Bead Array Normalization by NEighbourhood Residuals

## -- I --

identifyControlBeads | Classify each bead according to its control status
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

## -- L --

limmaDE | Differential expression using limma
limmaResults-class | Class "limmaResults"
LogFC | Class "limmaResults"
LogFC-method | Class "limmaResults"
LogFC<- | Class "limmaResults"
LogFC<--method | Class "limmaResults"
logGreenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.
LogOdds | Class "limmaResults"
LogOdds-method | Class "limmaResults"
LogOdds<- | Class "limmaResults"
LogOdds<--method | Class "limmaResults"
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.

## -- M --

makeControlProfile | Retrieve control beads
makeGEOSubmissionFiles | Create files for a Gene Expression Omnibus submission
makeQCTable | Tabulate QC scores
medianBackground | Image processing functions
medianNormalise | Median normalise data in a matrix
metaTemplate | GEO required fields
metrics | Accessing metrics information in bead-level objects
metrics-method | Accessing metrics information in bead-level objects

## -- N --

nObservations | Class "ExpressionSetIllumina"
nObservations-method | Class "ExpressionSetIllumina"
nObservations<- | Class "ExpressionSetIllumina"
nObservations<--method | Class "ExpressionSetIllumina"
noOutlierMethod | returns no outliers on an array section
normaliseIllumina | Normalise Illumina expression data
numBeads | Gets the number of beads from a beadLevelData object
numBeads-method | Class "beadLevelData"

## -- O --

outlierplot | Plot outlier locations

## -- P --

p95 | Accessing metrics information in bead-level objects
p95-method | Accessing metrics information in bead-level objects
platformSigs | Annotation definitions
plot-method | Class "limmaResults"
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
plotMA-method | Function to construct the classic MA plots from a dataset
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
PValue | Class "limmaResults"
PValue-method | Class "limmaResults"
PValue<- | Class "limmaResults"
PValue<--method | Class "limmaResults"

## -- Q --

qcData | Class "ExpressionSetIllumina"
qcData-method | Class "ExpressionSetIllumina"
quickSummary | Create summary values for specified IDs

## -- R --

readBeadSummaryData | Read BeadStudio gene expression output
readIdatFiles | Read BeadScan gene expression output
readIllumina | Read bead-level Illumina data
readLocsFile | Read ".locs" file.
readSampleSheet | Read a Sample sheet for a BeadArray experiment
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

## -- S --

sampleSheet | Read a Sample sheet for a BeadArray experiment
sampleSheet-method | Read a Sample sheet for a BeadArray experiment
sampleSheet<- | Read a Sample sheet for a BeadArray experiment
sampleSheet<--method | Read a Sample sheet for a BeadArray experiment
se.exprs-method | Class "ExpressionSetIllumina"
se.exprs<--method | Class "ExpressionSetIllumina"
sectionNames | Gets the section names from a beadLevelData Object
sectionNames-method | Class "beadLevelData"
setAnnotation | Deprecated Functions
setWeights | Set weights from BASH
show-method | Display object summary
showArrayMask | Show Array Mask
snr | Accessing metrics information in bead-level objects
snr-method | Accessing metrics information in bead-level objects
squeezedVarOutlierMethod | Identifier outliers on an array section
suggestAnnotation | Storage of annotation information
summarize | Create a summarized object

## -- W --

weightsOutlierMethod | returns all beads with weight=0.

## -- misc --

[-method | Class "ExpressionSetIllumina"
[-method | Class "limmaResults"
[[-method | Class "beadLevelData"