Quality assessment and low-level analysis for Illumina BeadArray data

Documentation for package ‘beadarray’ version 2.57.0

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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 --

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 --

returns all beads with weight=0.

-- misc --

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