| blima-package {blima} | R Documentation |
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.
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.
Vojtěch Kulvait Maintainer: VojtÄ›ch Kulvait <kulvait@gmail.com>