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.

AuthorMark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie
Date of publicationNone
MaintainerMark Dunning <Mark.Dunning@cruk.cam.ac.uk>
LicenseGPL-2
Version2.24.0

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

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