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

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.

Author
Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie
Date of publication
None
Maintainer
Mark Dunning <Mark.Dunning@cruk.cam.ac.uk>
License
GPL-2
Version
2.24.0

View on Bioconductor

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.

Files in this package

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