Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

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Documentation for package ‘blima’ version 1.43.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

blima-package	Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
aggregateAndPreprocess	Aggregate data
bacgroundCorrect	Data background correction.
bacgroundCorrectSingleArray	Data background correction.
backgroundChannelSubtract	Background channel subtraction
backgroundChannelSubtractSingleArray	Background channel subtraction
blima	Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.
channelExistsIntegrityWithLogicalVectorList	Internal function
checkIntegrity	Internal function
checkIntegrityLogical	Internal function
checkIntegrityOfListOfBeadLevelDataObjects	Internal function
checkIntegrityOfSingleBeadLevelDataObject	Internal function
chipArrayStatistics	Statistics of beadLevelData
createSummarizedMatrix	Summarized value matrix.
doAction	Internal function
doProbeTTests	T-test for probe level data.
doTTests	T-test for bead (detector) level data.
filterBg	Bg correct vector
getNextVector	Support probe and beadl level testing.
initMeanDistribution	initMeanDistribution
insertColumn	Internal function to support chipArrayStatistics
interpolateSortedVector	Interpolate sorted vector
interpolateSortedVectorRcpp_	interpolateSortedVectorRcpp
log2TransformPositive	Log2 transform of numbers >1.
meanDistribution	Produce sorted double vector with mean distribution.
nonParametricEstimator	INTERNAL FUNCTION Xie background correct.
nonPositiveCorrect	Correct non positive
nonPositiveCorrectSingleArray	Correct non positive
numberOfDistributionElements	Internal
performXieCorrection	INTERNAL FUNCTION Xie background correct.
plotBackgroundImageAfterCorrection	Plot background image after correction
plotBackgroundImageBeforeCorrection	Plot background image before correction
quantileNormalize	Bead level quantile normalization.
readToVector	Support doTTests function.
selectedChannelTransform	Channel transformation
selectedChannelTransformSingleArray	Channel transformation
singleArrayNormalize	Bead level quantile normalization.
singleChannelExistsIntegrityWithLogicalVector	Internal function
singleCheckIntegrityLogicalVector	Internal function
singleNumberOfDistributionElements	Internal
updateMeanDistribution	updateMeanDistribution
varianceBeadStabilise	Bead level VST.
varianceBeadStabiliseSingleArray	Bead level VST.
vstFromLumi	Function from LGPL lumi package 2.16.0
writeBackgroundImages	Write Background Images
xieBacgroundCorrect	Xie background correct.
xieBacgroundCorrectSingleArray	INTERNAL FUNCTION Xie background correct.