A B C D E G H I L M N O P Q R S W misc
beadarray-package | The beadarray package: a tool for low-level analysis of Illumina BeadArrays |
addFeatureData | Add probe data |
annotation-method | Storage of annotation information |
annotation<--method | Storage of annotation information |
arrayNames | Deprecated Functions |
arrayNames-method | Class "BeadLevelList" |
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 |
beadarrayUsersGuide | View beadarray User's Guide |
beadLevelData-class | Class "beadLevelData" |
BeadLevelList-class | Class "BeadLevelList" |
beadRegistrationData-class | Class "beadRegistrationData" |
beadStatusVector | Classify each bead according to its control status |
boxplot-method | Boxplots from summary data |
boxplot-method | Class "beadLevelData" |
boxplot-method | Class "beadRegistrationData" |
calculateDetection | Calculate detection scores |
calculateOutlierStats | Outlier distribution stats |
checkPlatform | Deprecated Functions |
checkRegistration | Perform check for misregistered array segments. |
combine-method | Combine two objects. |
combinedControlPlot | Flexible bead-level QC pipeline |
controlProbeDetection | Percentage of beads detected |
convertBeadLevelList | Convert a BeadLevelList object into a beadLevelData object |
createBeadSummaryData | Deprecated Functions |
createTargetsFile | A function to generate a targets file given a directory of Illumina bead-level files |
Detection | Class "ExpressionSetIllumina" |
Detection-method | Class "ExpressionSetIllumina" |
Detection<- | Class "ExpressionSetIllumina" |
Detection<--method | Class "ExpressionSetIllumina" |
dim-method | Retrieve the dimensions of an object |
expressionQCPipeline | Flexible bead-level QC pipeline |
ExpressionSetIllumina-class | Class "ExpressionSetIllumina" |
exprs-method | Class "ExpressionSetIllumina" |
exprs<--method | Class "ExpressionSetIllumina" |
generateNeighbours | Generate matrix of neighbouring beads |
genericBeadIntensityPlot | Plotting the intensities of selected beads on a section |
getAnnotation | Deprecated Functions |
getArrayData | Deprecated Functions |
getArrayData-method | Class "BeadLevelList" |
getBeadData | Get raw data from a beadLevelData object |
getControlProfile | Storage of annotation information |
greenChannel | Class "illuminaChannel" |
greenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
HULK | HULK - Bead Array Normalization by NEighbourhood Residuals |
identifyControlBeads | Classify each bead according to its control status |
illuminaBackground | Image processing functions |
illuminaChannel-class | Class "illuminaChannel" |
illuminaForeground | Image processing functions |
illuminaOutlierMethod | Identifier outliers on an array section |
illuminaSharpen | Image processing functions |
imageplot | imageplot for beadLevelData object |
insertBeadData | Add, modify or remove data in a beadLevelData object |
insertSectionData | Modify the sectionData slot |
logGreenChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
logRatioTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
logRedChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
makeControlProfile | Retrieve control beads |
makeQCTable | Tabulate QC scores |
medianBackground | Image processing functions |
medianNormalise | Median normalise data in a matrix |
metrics | Accessing metrics information in bead-level objects |
metrics-method | Accessing metrics information in bead-level objects |
nObservations | Class "ExpressionSetIllumina" |
nObservations-method | Class "ExpressionSetIllumina" |
nObservations<- | Class "ExpressionSetIllumina" |
nObservations<--method | Class "ExpressionSetIllumina" |
noOutlierMethod | returns no outliers on an array section |
normaliseIllumina | Normalise Illumina expression data |
numBeads | Gets the number of beads from a beadLevelData object |
numBeads-method | Class "beadLevelData" |
outlierplot | Plot outlier locations |
p95 | Accessing metrics information in bead-level objects |
p95-method | Accessing metrics information in bead-level objects |
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 |
plotMA | Scatter plots and MA-plots for all specified arrays |
plotMAXY | Scatter plots and MA-plots for all specified arrays |
plotTIFF | Produce plots of the Illumina tiff images |
plotXY | Scatter plots and MA-plots for all specified arrays |
poscontPlot | Plot the positive controls |
processSwathData | Prepare iScan data for use with beadarray |
qcData | Class "ExpressionSetIllumina" |
qcData-method | Class "ExpressionSetIllumina" |
quickSummary | Create summary values for specified IDs |
readBeadSummaryData | Read BeadStudio gene expression output |
readIllumina | Read bead-level Illumina data |
readLocsFile | Read ".locs" file. |
readSampleSheet | Read a Sample sheet for a BeadArray experiment |
readTIFF | Read the Illumina tiff images |
redChannelTransform | Functions for transforming the data store in a 'beadLevelData' object for easier visualisation or summarisation. |
removeBeadData | Add, modify or remove data in a beadLevelData object |
sampleSheet | Read a Sample sheet for a BeadArray experiment |
sampleSheet-method | Read a Sample sheet for a BeadArray experiment |
sampleSheet<- | Read a Sample sheet for a BeadArray experiment |
sampleSheet<--method | Read a Sample sheet for a BeadArray experiment |
se.exprs-method | Class "ExpressionSetIllumina" |
se.exprs<--method | Class "ExpressionSetIllumina" |
sectionNames | Gets the section names from a beadLevelData Object |
sectionNames-method | Class "beadLevelData" |
setAnnotation | Deprecated Functions |
setWeights | Set weights from BASH |
show-method | Display object summary |
showArrayMask | Show Array Mask |
snr | Accessing metrics information in bead-level objects |
snr-method | Accessing metrics information in bead-level objects |
squeezedVarOutlierMethod | Identifier outliers on an array section |
suggestAnnotation | Storage of annotation information |
summarize | Create a summarized object |
weightsOutlierMethod | returns all beads with weight=0. |
[-method | Class "ExpressionSetIllumina" |
[[-method | Class "beadLevelData" |