Quality assessment and low-level analysis for Illumina BeadArray data


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Documentation for package ‘beadarray’ version 1.14.0

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A B C D E F G H I L M N O P Q R S V misc

-- A --

addArrayMask Array Mask
arrayNames Gets the strip/array names from a BeadLevelList Object
arrayNames,BeadLevelList-method Class "BeadLevelList"

-- B --

backgroundControlPlot QA measures based on bead-level negative controls
backgroundCorrect Background correct a BeadLevelList object
backgroundCorrect,BeadLevelList,character,double,logical-method Class "BeadLevelList"
backgroundCorrect,BeadLevelList-method Background correct a BeadLevelList object
backgroundCorrect,RGList-method Background correct a BeadLevelList object
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
BeadChipSummary Interactive bead-level plotting
BeadLevelList Class "BeadLevelList"
BeadLevelList-class Class "BeadLevelList"
beadResids Calculates per strip/array bead-level residuals
BGFilter Background Filter
BGFilterWeighted Weighted Background Filter
BLData BeadLevelList objec from an example experiment
boxplotBeads Box plot of bead intensities
BSData ExpressionSetIllumina object for the example experiment

-- C --

calculateBeadLevelScores Quality assessment for expression chips
calculateDetection Calculate detection scores
chooseClusters Choose Clusters
class:ExpressionSetIllumina Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
clearArrayMask Array Mask
closeImage Close Image
combine,ExpressionSetIllumina,ANY-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combine,ExpressionSetIllumina,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combineBeadLevelLists Combines data from two BeadLevelList objects
combineBeadLevelLists,BeadLevelList-method Class "BeadLevelList"
copyBeadLevelList Copies a BeadLevelList Object
copyBeadLevelList,BeadLevelList-method Class "BeadLevelList"
createBeadSummaryData Produce bead averages

-- D --

denseRegions Find Dense Regions of Points (as used in diffuse defect analysis).
Detection Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection<- Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
dim,BeadLevelList-method Class "BeadLevelList"

-- E --

ExpressionControlData Control annotation for Illumina expression chips
ExpressionSetIllumina-class Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

-- F --

findAllOutliers Find outliers on a given strip/array
findBeadStatus Find Outliers

-- G --

generateE Generate Error Image for BeadLevelList object
generateNeighbours Generate Neighbours Matrix for BeadLevelList object
getAnnotation Storage of annotation information for Illumina expression chips
getArrayData Get raw data from a BeadLevelList object
getArrayData,BeadLevelList-method Class "BeadLevelList"
getControlAnno Storage of annotation information for Illumina expression chips
getProbeIntensities Find Outliers
getProbeIntensities,BeadLevelList-method Find Outliers
getVariance Gets the bead-type variances from an ExpressionSetIllumina Object
getVariance,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
gradientPlot Quality assessment for expression chips

-- H --

HULK HULK - Bead Array Normalization by NEighbourhood Residuals
HULKResids HULK - Residuals

-- I --

imageplot imageplot for BeadLevelList object
initialize,BeadLevelList-method Class "BeadLevelList"
initialize,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

-- L --

lmhPlot Plot the bead-level hybridisation controls

-- M --

medianNormalise Median normalise data in a matrix

-- N --

NoBeads Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads<- Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
normaliseIllumina Normalise Illumina expression data
numBeads Gets the number of beads from a BeadLevelList object
numBeads,BeadLevelList-method Class "BeadLevelList"

-- O --

outlierPlot Locations of outliers on an Illumina chip

-- P --

pData,BeadLevelList-method Class "BeadLevelList"
phenoData,BeadLevelList-method Class "BeadLevelList"
plotBeadDensities plot densities of bead intensities
plotBeadIntensities Plot bead intensities
plotBeadLocations Plot bead locations
plotMA Show MA plots
plotMAXY Scatter plots and MA-plots for all specified arrays
plotOnSAM Show variation between all 96 arrays
plotRG Plot bead-level data: R vs G intensities
plotTIFF Produce plots of the Illumina tiff images
plotXY XY plots for two samples
poscontPlot Plot bead-level housekeeping and biotin controls
probePairsPlot QA plot using perfect match and mismatch controls

-- Q --

qcBeadLevel Generate simple diagnostic plots for Illumina bead-level data
QCInfo Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo<- Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo<-,ExpressionSetIllumina,list-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.

-- R --

rankInvariantNormalise Rank Invariant normalise data in a matrix
readBeadSummaryData Read BeadStudio gene expression output
readBGX Read Illumina .bgx file into R
readIllumina Read bead-level data into R
readLocs Read the .locs file produced with each array
readQC Read Illumina control intensities
readTIFF Read the Illumina tiff images
removeArrayMask Array Mask

-- S --

SAMSummary Interactive bead-level plotting
se.exprs,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
se.exprs<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
setAnnotation Storage of annotation information for Illumina expression chips
setWeights Set BeadLevelList Weights
show,BeadLevelList-method Class "BeadLevelList"
show,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
showArrayMask Array Mask

-- V --

viewBeads View Beads

-- misc --

[,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[[,BeadLevelList,ANY,missing-method Class "BeadLevelList"