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: | 1.28.0 |
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_14 |
git_last_commit: | 2a638a4 |
git_last_commit_date: | 2021-10-26 |
Date/Publication: | 2021-10-26 |
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>