Quality assessment and low-level analysis for Illumina BeadArray data

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Documentation for package ‘beadarray’ version 2.43.0

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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"