Man pages for markdunning/beadarray
Quality assessment and low-level analysis for Illumina BeadArray data

addFeatureDataAdd probe data
annotationInterfaceStorage of annotation information
backgroundCorrectSingleSectionBackground correct an array-section
BASHBASH - BeadArray Subversion of Harshlight
BASHCompactBASH - Compact Defect Analysis
BASHDiffuseBASH - Diffuse Defect Analysis
BASHExtendedBASH - Extended Defect Analysis
beadarray-packageThe beadarray package: a tool for low-level analysis of...
beadarrayUsersGuideView beadarray User's Guide
boxplotBoxplots from summary data
calculateDetectionCalculate detection scores
calculateOutlierStatsOutlier distribution stats
checkRegistrationPerform check for misregistered array segments.
class-beadLevelDataClass "beadLevelData"
class-BeadLevelListClass "BeadLevelList"
class-beadRegistrationDataClass "beadRegistrationData"
class-ExpressionSetIlluminaClass "ExpressionSetIllumina"
class-illuminaChannelClass "illuminaChannel"
class-limmaResultsClass "limmaResults"
combineCombine two objects.
controlProbeDetectionPercentage of beads detected
convertBeadLevelListConvert a BeadLevelList object into a beadLevelData object
createTargetsFileA function to generate a targets file given a directory of...
deprecatedFunctionsDeprecated Functions
dimRetrieve the dimensions of an object
expressionQCPipelineFlexible bead-level QC pipeline
generateNeighboursGenerate matrix of neighbouring beads
GEOCreate files for a Gene Expression Omnibus submission
GEOtemplateGEO required fields
getBeadDataGet raw data from a beadLevelData object
HULKHULK - Bead Array Normalization by NEighbourhood Residuals
identifyControlBeadsClassify each bead according to its control status
illuminaOutlierMethodIdentifier outliers on an array section
imageplotimageplot for beadLevelData object
imageProcessingImage processing functions
insertBeadDataAdd, modify or remove data in a beadLevelData object
insertSectionDataModify the sectionData slot
limmaDEDifferential expression using limma
makeControlProfileRetrieve control beads
makeQCTableTabulate QC scores
maplotsFunction to construct the classic MA plots from a dataset
medianNormaliseMedian normalise data in a matrix
metricsAccessing metrics information in bead-level objects
noOutlierMethodreturns no outliers on an array section
normaliseIlluminaNormalise Illumina expression data
numBeadsGets the number of beads from a beadLevelData object
outlierplotPlot outlier locations
platformSigsAnnotation definitions
plotBeadIntensitiesPlotting the intensities of selected beads on a section
plotBeadLocationsPlot bead locations
plotChipLayoutFunction to Plot the Layout of an Illumina BeadChip
plotMAXYScatter plots and MA-plots for all specified arrays
plotTIFFProduce plots of the Illumina tiff images
poscontPlotPlot the positive controls
processSwathDataPrepare iScan data for use with beadarray
quickSummaryCreate summary values for specified IDs
readBeadSummaryDataRead BeadStudio gene expression output
readIdatFilesRead BeadScan gene expression output
readIlluminaRead bead-level Illumina data
readLocsFileRead ".locs" file.
readTIFFRead the Illumina tiff images
sampleSheetRead a Sample sheet for a BeadArray experiment
sectionNamesGets the section names from a beadLevelData Object
setWeightsSet weights from BASH
showDisplay object summary
showArrayMaskShow Array Mask
squeezedVarOutlierMethodIdentifier outliers on an array section
summarizeCreate a summarized object
transformationFunctionsFunctions for transforming the data store in a...
weightsOutlierMethodreturns all beads with weight=0.
markdunning/beadarray documentation built on Aug. 19, 2017, 9:10 p.m.