blima-package {blima} | R Documentation

## Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.

### Description

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 provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

### Details

The DESCRIPTION file:

Encoding: | UTF-8
Package: | blima
Type: | Package
Title: | Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
Version: | 1.22.0
Date: | 2017-09-23
Author: | Vojtech Kulvait
Maintainer: | Vojtech Kulvait <kulvait@gmail.com>
Description: | 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.
License: | GPL-3
LazyLoad: | yes
Depends: | R(>= 3.3)
Imports: | beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics
LinkingTo: | Rcpp
Suggests: | xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr
URL: | https://bitbucket.org/kulvait/blima
biocViews: | Microarray, Preprocessing, Normalization, DifferentialExpression, GeneRegulation, GeneExpression
VignetteBuilder: | knitr
git_url: | https://git.bioconductor.org/packages/blima
git_branch: | RELEASE_3_11
git_last_commit: | f8ad491
git_last_commit_date: | 2020-04-27
Date/Publication: | 2020-04-27

Index of help topics:

    aggregateAndPreprocess
                            Aggregate data
    bacgroundCorrect        Data background correction.
    bacgroundCorrectSingleArray
                            Data background correction.
    backgroundChannelSubtract
                            Background channel subtraction
    backgroundChannelSubtractSingleArray
                            Background channel subtraction
    blima-package           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.

### Author(s)

Vojtěch Kulvait Maintainer: VojtÄ›ch Kulvait <kulvait@gmail.com>

[Package blima version 1.22.0 Index]