Package: beadarray 2.57.0
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:
beadarray_2.57.0.tar.gz
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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')) |
- metaTemplate - GEO required fields
- platformSigs - Annotation definitions
On BioConductor:beadarray-2.57.0(bioc 3.21)beadarray-2.56.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarrayonechannelqualitycontrolpreprocessing
Last updated 2 months agofrom:21fcf33948. Checks:OK: 1 ERROR: 1 NOTE: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 10 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 10 2024 |
| R-4.5-linux-x86_64 | ERROR | Dec 10 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 10 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 10 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 10 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 10 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 10 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 10 2024 |
Exports:addFeatureDataannotationannotation<-ArrayWeightsArrayWeights<-backgroundCorrectSingleSectionBASHBASHCompactBASHDiffuseBASHExtendedbeadarrayUsersGuidebeadStatusVectorboxplotcalculateDetectioncalculateOutlierStatscheckPlatformcheckRegistrationcombinecombinedControlPlotContrastMatrixContrastMatrix<-controlProbeDetectionconvertBeadLevelListcreateGEOMatrixcreateGEOMetacreateTargetsFileDesignMatrixDesignMatrix<-DetectionDetection<-expressionQCPipelineexprsexprs<-generateNeighboursgenericBeadIntensityPlotgetAnnotationgetBeadDatagreenChannelgreenChannelTransformHULKidentifyControlBeadsilluminaBackgroundilluminaForegroundilluminaOutlierMethodilluminaSharpenimageplotinsertBeadDatainsertSectionDatalimmaDELogFCLogFC<-logGreenChannelTransformLogOddsLogOdds<-logRatioTransformlogRedChannelTransformmakeControlProfilemakeGEOSubmissionFilesmakeQCTablemedianBackgroundmedianNormalisemetricsnObservationsnObservations<-noOutlierMethodnormaliseIlluminanumBeadsoutlierplotp95plotBeadIntensitiesplotBeadLocationsplotChipLayoutplotMAXYplotTIFFposcontPlotprocessSwathDataPValuePValue<-qcDataquickSummaryreadBeadSummaryDatareadIdatFilesreadIlluminareadLocsFilereadSampleSheetreadTIFFredChannelTransformremoveBeadDatase.exprsse.exprs<-sectionNamessetAnnotationsetWeightsshowshowArrayMasksnrsqueezedVarOutlierMethodsuggestAnnotationsummarizeweightsOutlierMethod
Dependencies:AnnotationDbiaskpassbase64BeadDataPackRBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIfansifarverfastmapgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehexbinhttrilluminaioIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmamagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngR6RColorBrewerRcppreshape2rlangRSQLiteS4VectorsscalesstatmodstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Analysis of Bead-level Data using beadarray
Rendered frombeadlevel.Rmdusingknitr::rmarkdownon Dec 10 2024.Last update: 2024-06-17
Started: 2024-06-17
Analysis of bead-summary data
Rendered frombeadsummary.Rmdusingknitr::rmarkdownon Dec 10 2024.Last update: 2024-10-16
Started: 2024-06-17
Image Analysis with beadarray
Rendered fromImageProcessing.Rmdusingknitr::rmarkdownon Dec 10 2024.Last update: 2024-06-17
Started: 2024-06-17
beadarray
Rendered frombeadarray.Rmdusingknitr::rmarkdownon Dec 10 2024.Last update: 2024-10-17
Started: 2024-06-17
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 |
