Package: blima 1.39.0

Vojtěch Kulvait

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

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

Authors:Vojtěch Kulvait

blima_1.39.0.tar.gz
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blima.pdf |blima.html✨
blima/json (API)
NEWS

# Install 'blima' in R:
install.packages('blima', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://bitbucket.org/kulvait/blima

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:blima-1.39.0(bioc 3.20)blima-1.38.0(bioc 3.19)

bioconductor-package

15 exports 0.91 score 72 dependencies

Last updated 2 months agofrom:77bff79842

Exports:bacgroundCorrectbackgroundChannelSubtractchipArrayStatisticscreateSummarizedMatrixdoProbeTTestsdoTTestslog2TransformPositivenonPositiveCorrectplotBackgroundImageAfterCorrectionplotBackgroundImageBeforeCorrectionquantileNormalizeselectedChannelTransformvarianceBeadStabilisewriteBackgroundImagesxieBacgroundCorrect

Dependencies:AnnotationDbiaskpassbase64beadarrayBeadDataPackRBiobaseBiocGenericsBiostringsbitbit64blobcachemclicolorspacecpp11crayoncurlDBIfansifarverfastmapGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehexbinhttrilluminaioIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmamagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngR6RColorBrewerRcppreshape2rlangRSQLiteS4VectorsscalesstatmodstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

blima an R package for Bead Level Illumina Microarray Analysis

Rendered fromblima.rnwusingknitr::knitron Jun 30 2024.

Last update: 2017-09-23
Started: 2014-05-08

Readme and manuals

Help Manual

Help pageTopics
Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.blima-package blima
Aggregate dataaggregateAndPreprocess
Data background correction.bacgroundCorrect
Data background correction.bacgroundCorrectSingleArray
Background channel subtractionbackgroundChannelSubtract
Background channel subtractionbackgroundChannelSubtractSingleArray
Internal functionchannelExistsIntegrityWithLogicalVectorList
Internal functioncheckIntegrity
Internal functioncheckIntegrityLogical
Internal functioncheckIntegrityOfListOfBeadLevelDataObjects
Internal functioncheckIntegrityOfSingleBeadLevelDataObject
Statistics of beadLevelDatachipArrayStatistics
Summarized value matrix.createSummarizedMatrix
Internal functiondoAction
T-test for probe level data.doProbeTTests
T-test for bead (detector) level data.doTTests
Bg correct vectorfilterBg
Support probe and beadl level testing.getNextVector
initMeanDistributioninitMeanDistribution
Internal function to support chipArrayStatisticsinsertColumn
Interpolate sorted vectorinterpolateSortedVector
interpolateSortedVectorRcppinterpolateSortedVectorRcpp_
Log2 transform of numbers >1.log2TransformPositive
Produce sorted double vector with mean distribution.meanDistribution
INTERNAL FUNCTION Xie background correct.nonParametricEstimator
Correct non positivenonPositiveCorrect
Correct non positivenonPositiveCorrectSingleArray
InternalnumberOfDistributionElements
INTERNAL FUNCTION Xie background correct.performXieCorrection
Plot background image after correctionplotBackgroundImageAfterCorrection
Plot background image before correctionplotBackgroundImageBeforeCorrection
Bead level quantile normalization.quantileNormalize
Support doTTests function.readToVector
Channel transformationselectedChannelTransform
Channel transformationselectedChannelTransformSingleArray
Bead level quantile normalization.singleArrayNormalize
Internal functionsingleChannelExistsIntegrityWithLogicalVector
Internal functionsingleCheckIntegrityLogicalVector
InternalsingleNumberOfDistributionElements
updateMeanDistributionupdateMeanDistribution
Bead level VST.varianceBeadStabilise
Bead level VST.varianceBeadStabiliseSingleArray
Function from LGPL lumi package 2.16.0vstFromLumi
Write Background ImageswriteBackgroundImages
Xie background correct.xieBacgroundCorrect
INTERNAL FUNCTION Xie background correct.xieBacgroundCorrectSingleArray