beadarray: Quality assessment and low-level analysis for Illumina BeadArray data
Version 2.26.1

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

Browse man pages Browse package API and functions Browse package files

AuthorMark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie
Bioconductor views Microarray OneChannel Preprocessing QualityControl
Date of publicationNone
MaintainerMark Dunning <Mark.Dunning@cruk.cam.ac.uk>
LicenseGPL-2
Version2.26.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("beadarray")

Man pages

addFeatureData: Add probe data
annotationInterface: Storage of annotation information
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
beadarray-package: The beadarray package: a tool for low-level analysis of...
beadarrayUsersGuide: View beadarray User's Guide
boxplot: Boxplots from summary data
calculateDetection: Calculate detection scores
calculateOutlierStats: Outlier distribution stats
checkRegistration: Perform check for misregistered array segments.
class-beadLevelData: Class "beadLevelData"
class-BeadLevelList: Class "BeadLevelList"
class-beadRegistrationData: Class "beadRegistrationData"
class-ExpressionSetIllumina: Class "ExpressionSetIllumina"
class-illuminaChannel: Class "illuminaChannel"
class-limmaResults: Class "limmaResults"
combine: Combine two objects.
controlProbeDetection: Percentage of beads detected
convertBeadLevelList: Convert a BeadLevelList object into a beadLevelData object
createTargetsFile: A function to generate a targets file given a directory of...
deprecatedFunctions: Deprecated Functions
dim: Retrieve the dimensions of an object
expressionQCPipeline: Flexible bead-level QC pipeline
generateNeighbours: Generate matrix of neighbouring beads
GEO: Create files for a Gene Expression Omnibus submission
GEOtemplate: GEO required fields
getBeadData: Get raw data from a beadLevelData object
HULK: HULK - Bead Array Normalization by NEighbourhood Residuals
identifyControlBeads: Classify each bead according to its control status
illuminaOutlierMethod: Identifier outliers on an array section
imageplot: imageplot for beadLevelData object
imageProcessing: Image processing functions
insertBeadData: Add, modify or remove data in a beadLevelData object
insertSectionData: Modify the sectionData slot
limmaDE: Differential expression using limma
makeControlProfile: Retrieve control beads
makeQCTable: Tabulate QC scores
maplots: Function to construct the classic MA plots from a dataset
medianNormalise: Median normalise data in a matrix
metrics: Accessing metrics information in bead-level objects
noOutlierMethod: returns no outliers on an array section
normaliseIllumina: Normalise Illumina expression data
numBeads: Gets the number of beads from a beadLevelData object
outlierplot: Plot outlier locations
platformSigs: Annotation definitions
plotBeadIntensities: Plotting the intensities of selected beads on a section
plotBeadLocations: Plot bead locations
plotChipLayout: Function to Plot the Layout of an Illumina BeadChip
plotMAXY: Scatter plots and MA-plots for all specified arrays
plotTIFF: Produce plots of the Illumina tiff images
poscontPlot: Plot the positive controls
processSwathData: Prepare iScan data for use with beadarray
quickSummary: Create summary values for specified IDs
readBeadSummaryData: Read BeadStudio gene expression output
readIdatFiles: Read BeadScan gene expression output
readIllumina: Read bead-level Illumina data
readLocsFile: Read ".locs" file.
readTIFF: Read the Illumina tiff images
sampleSheet: Read a Sample sheet for a BeadArray experiment
sectionNames: Gets the section names from a beadLevelData Object
setWeights: Set weights from BASH
show: Display object summary
showArrayMask: Show Array Mask
squeezedVarOutlierMethod: Identifier outliers on an array section
summarize: Create a summarized object
transformationFunctions: Functions for transforming the data store in a...
weightsOutlierMethod: returns all beads with weight=0.

Functions

ArrayWeights Man page
ArrayWeights,limmaResults-method Man page
ArrayWeights<- Man page
ArrayWeights<-,limmaResults,numeric-method Man page
BASH Man page Source code
BASHCompact Man page Source code
BASHDiffuse Man page Source code
BASHExtended Man page Source code
BGFilter Source code
BGFilterWeighted Source code
BeadLevelList Man page
BeadLevelList-class Man page
ContrastMatrix Man page
ContrastMatrix,limmaResults-method Man page
ContrastMatrix<- Man page
ContrastMatrix<-,limmaResults,matrix-method Man page
DesignMatrix Man page
DesignMatrix,limmaResults-method Man page
DesignMatrix<- Man page
DesignMatrix<-,limmaResults,matrix-method Man page
Detection Man page
Detection,ExpressionSetIllumina-method Man page
Detection<- Man page
Detection<-,ExpressionSetIllumina,matrix-method Man page
ExpressionSetIllumina-class Man page
HULK Man page Source code
HULKResids Source code
LogFC Man page
LogFC,limmaResults-method Man page
LogFC<- Man page
LogFC<-,limmaResults,matrix-method Man page
LogOdds Man page
LogOdds,limmaResults-method Man page
LogOdds<- Man page
LogOdds<-,limmaResults,matrix-method Man page
PValue Man page
PValue,limmaResults-method Man page
PValue<- Man page
PValue<-,limmaResults,matrix-method Man page
[,ExpressionSetIllumina,ANY-method Man page
[,ExpressionSetIllumina-method Man page
[,limmaResults-method Man page
[[,beadLevelData,ANY,missing-method Man page
addFeatureData Man page Source code
analyseDirectory Source code
annotation Man page
annotation,ExpressionSetIllumina-method Man page
annotation,beadLevelData-method Man page
annotation<-,ExpressionSetIllumina,character-method Man page
annotation<-,beadLevelData,character-method Man page
appendHistory Source code
arrayNames Man page
arrayNames,BeadLevelList-method Man page
assignSegments Source code
assignToImage Source code
backgroundCorrectSingleSection Man page Source code
beadLevelData-class Man page
beadRegistrationData-class Man page
beadStatusVector Man page Source code
beadarray-package Man page
beadarrayUsersGuide Man page Source code
beadsNearNonDecoded Source code
boxplot,ExpressionSetIllumina-method Man page
boxplot,beadLevelData-method Man page
boxplot,beadRegistrationData-method Man page
calculateDetection Man page Source code
calculateOutlierStats Man page Source code
checkPlatform Man page Source code
checkRegistration Man page Source code
checkSwathStatus Source code
chooseClusters Source code
closeImage Source code
combine,ExpressionSetIllumina,ExpressionSetIllumina-method Man page Man page
combine,beadLevelData,beadLevelData-method Man page
combine,limmaResults,limmaResults-method Man page
combinedControlPlot Man page Source code
controlProbeDetection Man page Source code
convertBeadLevelList Man page Source code
createBeadSummaryData Man page
createGEOMatrix Man page Source code
createGEOMeta Man page Source code
createTargetsFile Man page Source code
denseRegions Source code
dim,ExpressionSetIllumina-method Man page
dim,beadLevelData-method Man page
dim,limmaResults-method Man page
duplicateSpots_2swaths Source code
expressionQCPipeline Man page Source code
exprs,ExpressionSetIllumina-method Man page
exprs<-,ExpressionSetIllumina,matrix-method Man page
findAllOutliersE Source code
findAllOutliersIgnore Source code
genSwaths Source code
genThreeSwaths Source code
genTwoSwaths Source code
generateE Source code
generateNeighbours Man page Source code
genericBeadIntensityPlot Man page Source code
getAnnotation Man page Source code
getArrayData Man page
getArrayData,BeadLevelList-method Man page
getBeadData Man page Source code
getControlProfile Man page
getPlatformSigs Source code
getSectionData Source code
getnextXMLtoken Source code
givenrow Source code
greenChannel Man page
greenChannelTransform Man page Source code
gridShift Source code
gridToLocsIndices Source code
identifyControlBeads Man page Source code
illuminaBackground Man page Source code
illuminaChannel-class Man page
illuminaForeground Man page Source code
illuminaForeground_6x6 Source code
illuminaOutlierMethod Man page Source code Source code
illuminaSharpen Man page Source code
imageplot Man page Source code
insertBeadData Man page Source code
insertSectionData Man page Source code
limmaDE Man page Source code
limmaResults-class Man page
locsIndicesToGrid Source code
log2.na Source code Source code
log2cap Source code
logGreenChannelTransform Man page Source code
logRatioTransform Man page Source code
logRedChannelTransform Man page Source code
makeControlProfile Man page Source code
makeGEOSubmissionFiles Man page Source code
makeQCTable Man page Source code
makeReport Source code
maplots Source code
mean.na Source code
medianBackground Man page Source code
medianNormalise Man page Source code
mergeAssayData Source code
mergePhenodata Source code
metaTemplate Man page
metrics Man page
metrics,beadLevelData-method Man page
nObservations Man page
nObservations,ExpressionSetIllumina-method Man page
nObservations<- Man page
nObservations<-,ExpressionSetIllumina,matrix-method Man page
neighboursFromLocs Source code
neighboursMatrixForAll Source code
noOutlierMethod Man page Source code
normaliseIllumina Man page Source code
numBeads Man page
numBeads,beadLevelData-method Man page
numberOfChannels Source code
numberOfColumns Source code
obtainLocs Source code
onAttach Source code
openTIFF Source code
outlierplot Man page Source code
outlierplot2 Source code
p95 Man page
p95,beadLevelData,character-method Man page
platformSigs Man page
plot,limmaResults-method Man page
plot.smooth.line Source code
plotBeadIntensities Man page Source code
plotBeadLocations Man page Source code
plotBeadLocations2 Source code
plotChipLayout Man page Source code
plotMA Man page
plotMA,ExpressionSetIllumina-method Man page
plotMAXY Man page Source code
plotProbe Source code
plotTIFF Man page Source code
plotXY Man page
poscontPlot Man page Source code
processSwathData Man page Source code
qcData Man page
qcData,ExpressionSetIllumina-method Man page
quickSummary Man page Source code
rankInvariantNormalise Source code
readBeadLevelTextFile Source code
readBeadSummaryData Man page Source code
readIdatFiles Man page Source code
readIllumina Man page Source code
readLocsFile Man page Source code
readQC Source code
readSampleSheet Man page Source code Source code
readTIFF Man page Source code
redChannelTransform Man page Source code
removeBeadData Man page Source code
sampleSheet Man page
sampleSheet,ExpressionSetIllumina-method Man page
sampleSheet,beadLevelData-method Man page
sampleSheet<- Man page
sampleSheet<-,ExpressionSetIllumina,data.frame-method Man page
sampleSheet<-,beadLevelData,data.frame-method Man page
scoreRegistration Source code
sd.na Source code
se.exprs,ExpressionSetIllumina-method Man page
se.exprs<-,ExpressionSetIllumina,matrix-method Man page
sectionNames Man page
sectionNames,beadLevelData-method Man page
setAnnotation Man page Source code
setFeatureData Source code
setWeights Man page Source code
show,ExpressionSetIllumina-method Man page
show,beadLevelData-method Man page
show,beadRegistrationData-method Man page
show,limmaResults-method Man page
showArrayMask Man page Source code
showArrayMask2 Source code
simpleXMLparse Source code
singleBeadIntensity Source code
singleBeadIntensity_6x6 Source code
snr Man page
snr,beadLevelData,character-method Man page
squeezedVarOutlierMethod Man page Source code
suggestAnnotation Man page Source code
suggestAnnotation_Vector Source code
summarize Man page Source code
takeclusterexpand Source code
testGridShift Source code
trimWhiteSpace Source code
uniqueProbeList Source code Source code
viewBeads Source code
weightsOutlierMethod Man page Source code
writeOutFiles Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/BASH.R
R/ExpressionSetIlluminaNormalisation.R
R/ExpressionSetIlluminaPlotting.R
R/ExpressionSetIllumina_calculateDetection.R
R/GEO.R
R/HULK.R
R/analyseDirectory.R
R/annotation.R
R/appendHistory.R
R/beadLevelData_QC.R
R/beadLevelData_[[.R
R/beadLevelData_assignSegments.R
R/beadLevelData_backgroundCorrect.R
R/beadLevelData_combine.R
R/beadLevelData_combinedQCPlot.R
R/beadLevelData_dim.R
R/beadLevelData_expressionQCPipeline.R
R/beadLevelData_getBeadData.R
R/beadLevelData_metrics.R
R/beadLevelData_numBeads.R
R/beadLevelData_outlierPlot.R
R/beadLevelData_plotBeadLocations.R
R/beadLevelData_sectionData.R
R/beadLevelData_sectionNames.R
R/beadLevelData_setWeights.R
R/beadLevelData_show.R
R/beadLevelData_showArrayMask.R
R/beadLevelData_spatialPlot.R
R/beadLevelData_summarize.R
R/beadLevelData_uniqueProbeList.R
R/boxplot.R
R/checkRegistration.R
R/convertBeadLevelList.R
R/createTargetsFile.R
R/experimental.R
R/expressionSetIllumina_channel.R
R/expressionSetIllumina_channelNames.R
R/getnextXMLtoken.R
R/gridPositionsFromLocs.R
R/illuminaChannel_initialize.R
R/imageProcessing.R
R/imageplot.R
R/insertBeadData.R
R/limmaDE.R
R/methods-ExpressionSetIllumina.R
R/methods-beadRegistrationData.R
R/methods-limmaResults.R
R/miscFunctions.R
R/nearNonDecodedRegion.R
R/obtainLocs.R
R/outlierMethods.R
R/plotChipLayout.R
R/plotTIFF.R
R/readBeadLevelTextFile.R
R/readBeadSummaryData.R
R/readIdatFiles.R
R/readIllumina.R
R/readLocsFile.R
R/readSampleSheet.R
R/readTIFF.R
R/reports.R
R/sampleSheet.R
R/simpleXMLparse.R
R/standardIlluminaChannels.R
R/swathData_assignToImage.R
R/swathData_checkSwathStatus.R
R/swathData_genSwaths.R
R/swathData_processData.R
R/swathData_singleBeadIntensity.R
R/swathData_writeFiles.R
R/zzz.R
build
build/vignette.rds
data
data/datalist
data/metaTemplate.rda
data/platformSigs.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ImageProcessing.R
inst/doc/ImageProcessing.pdf
inst/doc/ImageProcessing.rnw
inst/doc/beadarray.R
inst/doc/beadarray.pdf
inst/doc/beadarray.rnw
inst/doc/beadlevel.R
inst/doc/beadlevel.pdf
inst/doc/beadlevel.rnw
inst/doc/beadsummary.R
inst/doc/beadsummary.pdf
inst/doc/beadsummary.rnw
man
man/BASH.Rd
man/BASHCompact.Rd
man/BASHDiffuse.Rd
man/BASHExtended.Rd
man/GEO.Rd
man/GEOtemplate.Rd
man/HULK.Rd
man/addFeatureData.Rd
man/annotationInterface.Rd
man/backgroundCorrectSingleSection.Rd
man/beadarray-package.Rd
man/beadarrayUsersGuide.Rd
man/boxplot.Rd
man/calculateDetection.Rd
man/calculateOutlierStats.Rd
man/checkRegistration.Rd
man/class-BeadLevelList.Rd
man/class-ExpressionSetIllumina.Rd
man/class-beadLevelData.Rd
man/class-beadRegistrationData.Rd
man/class-illuminaChannel.Rd
man/class-limmaResults.Rd
man/combine.Rd
man/controlProbeDetection.Rd
man/convertBeadLevelList.Rd
man/createTargetsFile.Rd
man/deprecatedFunctions.Rd
man/dim.Rd
man/expressionQCPipeline.Rd
man/generateNeighbours.Rd
man/getBeadData.Rd
man/identifyControlBeads.Rd
man/illuminaOutlierMethod.Rd
man/imageProcessing.Rd
man/imageplot.Rd
man/insertBeadData.Rd
man/insertSectionData.Rd
man/limmaDE.Rd
man/makeControlProfile.Rd
man/makeQCTable.Rd
man/maplots.Rd
man/medianNormalise.Rd
man/metrics.Rd
man/noOutlierMethod.Rd
man/normaliseIllumina.Rd
man/numBeads.Rd
man/outlierplot.Rd
man/platformSigs.Rd
man/plotBeadIntensities.Rd
man/plotBeadLocations.Rd
man/plotChipLayout.Rd
man/plotMAXY.Rd
man/plotTIFF.Rd
man/poscontPlot.Rd
man/processSwathData.Rd
man/quickSummary.Rd
man/readBeadSummaryData.Rd
man/readIdatFiles.Rd
man/readIllumina.Rd
man/readLocsFile.Rd
man/readTIFF.Rd
man/sampleSheet.Rd
man/sectionNames.Rd
man/setWeights.Rd
man/show.Rd
man/showArrayMask.Rd
man/squeezedVarOutlierMethod.Rd
man/summarize.Rd
man/transformationFunctions.Rd
man/weightsOutlierMethod.Rd
src
src/BASH.c
src/HULK.c
src/beadarray.h
src/determiningGridPositions.c
src/findAllOutliers.c
src/imageProcessing.c
vignettes
vignettes/ImageProcessing.rnw
vignettes/beadarray.bib
vignettes/beadarray.rnw
vignettes/beadlevel.rnw
vignettes/beadsummary.rnw
beadarray documentation built on May 23, 2017, 10:02 a.m.