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: 1.16.0
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_8
git_last_commit: b368eaf
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30

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 1.16.0 Index]