Package: beadarray 2.55.1

Mark Dunning

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.

Authors:Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie

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beadarray.pdf |beadarray.html✨
beadarray/json (API)
NEWS

# Install 'beadarray' in R:

install.packages('beadarray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

metaTemplate - GEO required fields
platformSigs - Annotation definitions

On BioConductor:beadarray-2.55.0(bioc 3.20)beadarray-2.54.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

100 exports 1.80 score 71 dependencies 4 dependents 94 mentions

Last updated 23 days agofrom:e5d12b7dc3

Exports:addFeatureData annotation annotation<-ArrayWeights ArrayWeights<-backgroundCorrectSingleSection BASH BASHCompact BASHDiffuse BASHExtended beadarrayUsersGuide beadStatusVector boxplot calculateDetection calculateOutlierStats checkPlatform checkRegistration combine combinedControlPlot ContrastMatrix ContrastMatrix<-controlProbeDetection convertBeadLevelList createGEOMatrix createGEOMeta createTargetsFile DesignMatrix DesignMatrix<-Detection Detection<-expressionQCPipeline exprs exprs<-generateNeighbours genericBeadIntensityPlot getAnnotation getBeadData greenChannel greenChannelTransform HULK identifyControlBeads illuminaBackground illuminaForeground illuminaOutlierMethod illuminaSharpen imageplot insertBeadData insertSectionData limmaDE LogFC LogFC<-logGreenChannelTransform LogOdds LogOdds<-logRatioTransform logRedChannelTransform makeControlProfile makeGEOSubmissionFiles makeQCTable medianBackground medianNormalise metrics nObservations nObservations<-noOutlierMethod normaliseIllumina numBeads outlierplot p95 plotBeadIntensities plotBeadLocations plotChipLayout plotMAXY plotTIFF poscontPlot processSwathData PValue PValue<-qcData quickSummary readBeadSummaryData readIdatFiles readIllumina readLocsFile readSampleSheet readTIFF redChannelTransform removeBeadData se.exprs se.exprs<-sectionNames setAnnotation setWeights show showArrayMask snr squeezedVarOutlierMethod suggestAnnotation summarize weightsOutlierMethod

Dependencies:AnnotationDbi askpass base64 BeadDataPackR Biobase BiocGenerics Biostrings bit bit64 blob cachem cli colorspace cpp11 crayon curl DBI fansi farver fastmap GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable hexbin httr illuminaio IRanges isoband jsonlite KEGGREST labeling lattice lifecycle limma magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png R6 RColorBrewer Rcpp reshape2 rlang RSQLite S4Vectors scales statmod stringi stringr sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The beadarray package: a tool for low-level analysis of Illumina BeadArrays	beadarray-package
Add probe data	addFeatureData
Storage of annotation information	annotation annotation,beadLevelData-method annotation,ExpressionSetIllumina-method annotation<-,beadLevelData,character-method annotation<-,ExpressionSetIllumina,character-method getControlProfile suggestAnnotation
Background correct an array-section	backgroundCorrectSingleSection
BASH - BeadArray Subversion of Harshlight	BASH
BASH - Compact Defect Analysis	BASHCompact
BASH - Diffuse Defect Analysis	BASHDiffuse
BASH - Extended Defect Analysis	BASHExtended
View beadarray User's Guide	beadarrayUsersGuide
Plotting the intensities of selected beads on a section	genericBeadIntensityPlot plotBeadIntensities
Class "beadLevelData"	beadLevelData-class boxplot,beadLevelData-method numBeads,beadLevelData-method sectionNames,beadLevelData-method [[,beadLevelData,ANY,missing-method
Class "BeadLevelList"	arrayNames,BeadLevelList-method BeadLevelList-class getArrayData,BeadLevelList-method
Class "beadRegistrationData"	beadRegistrationData-class boxplot,beadRegistrationData-method
Boxplots from summary data	boxplot,ExpressionSetIllumina-method
Calculate detection scores	calculateDetection
Outlier distribution stats	calculateOutlierStats
Perform check for misregistered array segments.	checkRegistration
Combine two objects.	combine,beadLevelData,beadLevelData-method combine,ExpressionSetIllumina,ExpressionSetIllumina-method
Percentage of beads detected	controlProbeDetection
Convert a BeadLevelList object into a beadLevelData object	convertBeadLevelList
A function to generate a targets file given a directory of Illumina bead-level files	createTargetsFile
Deprecated Functions	arrayNames checkPlatform createBeadSummaryData getAnnotation getArrayData setAnnotation
Retrieve the dimensions of an object	dim,beadLevelData-method dim,ExpressionSetIllumina-method
Flexible bead-level QC pipeline	combinedControlPlot expressionQCPipeline
Class "ExpressionSetIllumina"	Detection Detection,ExpressionSetIllumina-method Detection<- Detection<-,ExpressionSetIllumina,matrix-method ExpressionSetIllumina-class exprs,ExpressionSetIllumina-method exprs<-,ExpressionSetIllumina,matrix-method nObservations nObservations,ExpressionSetIllumina-method nObservations<- nObservations<-,ExpressionSetIllumina,matrix-method qcData qcData,ExpressionSetIllumina-method se.exprs,ExpressionSetIllumina-method se.exprs<-,ExpressionSetIllumina,matrix-method [,ExpressionSetIllumina,ANY-method [,ExpressionSetIllumina-method
Generate matrix of neighbouring beads	generateNeighbours
Get raw data from a beadLevelData object	getBeadData
HULK - Bead Array Normalization by NEighbourhood Residuals	HULK
Classify each bead according to its control status	beadStatusVector identifyControlBeads
Class "illuminaChannel"	greenChannel illuminaChannel-class
Identifier outliers on an array section	illuminaOutlierMethod
imageplot for beadLevelData object	imageplot
Image processing functions	illuminaBackground illuminaForeground illuminaSharpen medianBackground
Add, modify or remove data in a beadLevelData object	insertBeadData removeBeadData
Modify the sectionData slot	insertSectionData
Differential expression using limma	limmaDE
Class "limmaResults"	ArrayWeights ArrayWeights,limmaResults-method ArrayWeights<- ArrayWeights<-,limmaResults,numeric-method ContrastMatrix ContrastMatrix,limmaResults-method ContrastMatrix<- ContrastMatrix<-,limmaResults,matrix-method DesignMatrix DesignMatrix,limmaResults-method DesignMatrix<- DesignMatrix<-,limmaResults,matrix-method dim,limmaResults-method limmaResults-class LogFC LogFC,limmaResults-method LogFC<- LogFC<-,limmaResults,matrix-method LogOdds LogOdds,limmaResults-method LogOdds<- LogOdds<-,limmaResults,matrix-method plot,limmaResults-method PValue PValue,limmaResults-method PValue<- PValue<-,limmaResults,matrix-method [,limmaResults-method
Create files for a Gene Expression Omnibus submission	createGEOMatrix createGEOMeta makeGEOSubmissionFiles
Retrieve control beads	makeControlProfile
Tabulate QC scores	makeQCTable
Median normalise data in a matrix	medianNormalise
GEO required fields	metaTemplate
Accessing metrics information in bead-level objects	metrics metrics,beadLevelData-method p95 p95,beadLevelData,character-method snr snr,beadLevelData,character-method
returns no outliers on an array section	noOutlierMethod
Normalise Illumina expression data	normaliseIllumina
Gets the number of beads from a beadLevelData object	numBeads
Plot outlier locations	outlierplot
Annotation definitions	platformSigs
Plot bead locations	plotBeadLocations
Function to Plot the Layout of an Illumina BeadChip	plotChipLayout
Function to construct the classic MA plots from a dataset	plotMA,ExpressionSetIllumina-method
Scatter plots and MA-plots for all specified arrays	plotMA plotMAXY plotXY
Produce plots of the Illumina tiff images	plotTIFF
Plot the positive controls	poscontPlot
Prepare iScan data for use with beadarray	processSwathData
Create summary values for specified IDs	quickSummary
Read BeadStudio gene expression output	readBeadSummaryData
Read BeadScan gene expression output	readIdatFiles
Read bead-level Illumina data	readIllumina
Read ``.locs'' file.	readLocsFile
Read a Sample sheet for a BeadArray experiment	readSampleSheet sampleSheet sampleSheet,beadLevelData-method sampleSheet,ExpressionSetIllumina-method sampleSheet<- sampleSheet<-,beadLevelData,data.frame-method sampleSheet<-,ExpressionSetIllumina,data.frame-method
Read the Illumina tiff images	readTIFF
Gets the section names from a beadLevelData Object	sectionNames
Set weights from BASH	setWeights
Display object summary	show,beadLevelData-method show,beadRegistrationData-method show,ExpressionSetIllumina-method show,limmaResults-method
Show Array Mask	showArrayMask
Identifier outliers on an array section	squeezedVarOutlierMethod
Create a summarized object	summarize
Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation.	greenChannelTransform logGreenChannelTransform logRatioTransform logRedChannelTransform redChannelTransform
returns all beads with weight=0.	weightsOutlierMethod