Package: lumi 2.59.0

Lei Huang

lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

Authors:Pan Du, Richard Bourgon, Gang Feng, Simon Lin

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lumi.pdf |lumi.html✨
lumi/json (API)
NEWS

# Install 'lumi' in R:

install.packages('lumi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example.lumi - Example Illumina Expression data in LumiBatch class
example.lumiMethy - Example Illumina Infinium Methylation data in MethyLumiM class
example.methyTitration - Example Illumina Infinium Methylation titration data in MethyLumiM class

On BioConductor:lumi-2.59.0(bioc 3.21)lumi-2.58.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray onechannel preprocessing dnamethylation qualitycontrol twochannel

6.52 score 9 packages 290 scripts 2.1k downloads 238 mentions 97 exports 155 dependencies

Last updated 2 months agofrom:130abf107a. Checks:OK: 1 ERROR: 1 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	ERROR	Dec 20 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Dec 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Dec 18 2024

Exports:addAnnotationInfo addControlData2lumi addControlData2methyLumiM addNuId2lumi addNuID2lumi adjColorBias.quantile adjColorBias.ssn asBigMatrix beadNum beadNum<-beta2m bgAdjust bgAdjustMethylation boxplot boxplotColorBias coerce colorBiasSummary combine controlData controlData<-density detection detection<-detectionCall detectOutlier estimateBeta estimateIntensity estimateLumiCV estimateM estimateMethylationBG exprs exprs<-gammaFitEM getChipInfo getChrInfo getControlData getControlProbe getControlType getHistory getNuIDMappingInfo hist id2seq IlluminaID2nuID importMethyIDAT inverseVST is.nuID lumiB lumiExpresso lumiMethyB lumiMethyC lumiMethyN lumiMethyR lumiMethyStatus lumiN lumiQ lumiR lumiR.batch lumiT m2beta MAplot methylationCall normalizeMethylation.quantile normalizeMethylation.ssn nuID2EntrezID nuID2IlluminaID nuID2probeID nuID2RefSeqID nuID2targetID pairs plot plotCDF plotColorBias1D plotColorBias2D plotControlData plotDensity plotGammaFit plotHousekeepingGene plotSampleRelation plotStringencyGene plotVST probeID2nuID produceGEOPlatformFile produceGEOSampleInfoTemplate produceGEOSubmissionFile produceMethylationGEOSubmissionFile rankinvariant rsn sampleNames<-se.exprs se.exprs<-seq2id show smoothQuantileNormalization ssn summary targetID2nuID vst

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest doRNG dplyr fansi farver fastmap FDb.InfiniumMethylation.hg19 foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable HDF5Array hms httr httr2 illuminaio IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi multtest munsell nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scales scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml zlibbioc

Help page	Topics
A package for preprocessing Illumina microarray data	lumi-package lumi
Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray	addAnnotationInfo
Add the control probe data into the controlData slot of LumiBatch object	addControlData2lumi
Add methylation control data to a MethyLumiM object	addControlData2methyLumiM
Add the nuID information to the LumiBatch object	addNuID2lumi addNuId2lumi
Color bias adjustment of Illumina Infinium methylaton microarrays using smooth quantile normalization	adjColorBias.quantile
Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization	adjColorBias.ssn
convert the data matrix in the assayData of a ExpressionSet as BigMatrix	asBigMatrix asBigMatrix,ExpressionSet-method asBigMatrix-methods
Convert methylation Beta-value to M-value	beta2m
Background adjustment for Illumina data	bgAdjust
Estimate and adjust the background levels of Illumina Infinium methylaton microarrays	bgAdjustMethylation
boxplot of a ExpressionSet object	boxplot,ExpressionSet-method boxplot-methods boxplot.ExpressionSet
boxplot of a MethyLumiM object	boxplot,MethyLumiM-method
Plot the Illumina Infinium methylation color bias in terms of boxplot	boxplotColorBias
A summary of colorBias information	colorBiasSummary
Density plot of a ExpressionSet object	density,ExpressionSet-method density-methods density.ExpressionSet
Estimate the detectable probe ratio	detectionCall
Detect the outlier sample (or gene)	detectOutlier
Estimate methylation Beta-value matrix	estimateBeta
Estimate intensity of Illumina methylation data	estimateIntensity
Estimate the coefficient of variance matrix of LumiBatch object	estimateLumiCV
Estimate methylation M-value matrix	estimateM
Estimate the background levels of Illumina Infinium methylaton microarrays	estimateMethylationBG
Example Illumina Expression data in LumiBatch class	example.lumi
Example Illumina Infinium Methylation data in MethyLumiM class	example.lumiMethy
Example Illumina Infinium Methylation titration data in MethyLumiM class	example.methyTitration
Estimate the methylation status by fitting a Gamma mixture model using EM algorithm	gammaFitEM
Get Illumina Chip Information based on probe identifiers	getChipInfo
get the chromosome location information of methylation probes	getChrInfo
Get control probe information	getControlData
Get the control probe Ids	getControlProbe
Get the types of the control probes	getControlType
get the mapping information from nuID to RefSeq ID	getNuIDMappingInfo
Density plot of a ExpressionSet object	hist,ExpressionSet-method hist-methods hist.ExpressionSet
Transfer a nuID as a nucleotide sequence	id2seq
Matching Illumina IDs to nuID based on Illumina ID mapping library	IlluminaID2nuID
Import Illumina methylation .idat files as an MethyLumiM object	importMethyIDAT
Inverse VST transform	inverseVST
nuID self-identification	is.nuID
Background correction of Illumina Expression data	lumiB
Class LumiBatch: contain and describe Illumina microarray data	beadNum beadNum,ExpressionSet-method beadNum<- beadNum<-,ExpressionSet,ANY-method beadNum<-,ExpressionSet-method class:LumiBatch combine,ExpressionSet,LumiBatch-method combine,LumiBatch,ExpressionSet-method combine,LumiBatch,LumiBatch-method controlData controlData,LumiBatch-method controlData<- controlData<-,LumiBatch,ANY-method controlData<-,LumiBatch-method detection detection,ExpressionSet-method detection<- detection<-,ExpressionSet,ANY-method detection<-,ExpressionSet-method getHistory getHistory,LumiBatch-method initialize,LumiBatch-method LumiBatch LumiBatch-class sampleNames<-,LumiBatch,ANY-method se.exprs se.exprs,ExpressionSet-method se.exprs<- se.exprs<-,ExpressionSet,ANY-method se.exprs<-,ExpressionSet-method show,LumiBatch-method summary,LumiBatch-method [,LumiBatch,ANY,ANY,ANY-method [,LumiBatch-method
From raw Illumina probe intensities to expression values	lumiExpresso
Adjust background level of Illumina Infinium methylation data	lumiMethyB
Color bias adjust of Illumina Infinium methylation data	lumiMethyC
Normalize the Illumina Infinium methylation data	lumiMethyN
Reading Illumina methylation microarray data	lumiMethyR
Estimate the methylation status of individual methylation sites	lumiMethyStatus
Between chip normalization of a LumiBatch object	lumiN
Quality control evaluation of the LumiBatch object	lumiQ
Read in Illumina expression data	lumiR
Read BeadStudio output files in batch	lumiR.batch
Transfer the Illumina data to stabilize the variance	lumiT
Convert methylation M-value to Beta-value	m2beta
MAplot of a ExpressionSet object	MAplot MAplot,ExpressionSet-method MAplot-methods MAplot.ExpressionSet
Estimated methylation call	methylationCall
Monotonic smooth method	monoSmu
Fitting a curve with monotonic spline	monoSpline
Quantile normalization of Illumina Infinium methylation data at probe level	normalizeMethylation.quantile
Shift and scaling normalization of Illumina Infinium methylation data at probe level	normalizeMethylation.ssn
Map nuID to Entrez ID	nuID2EntrezID
Matching nuIDs to Illumina IDs based on Illumina ID mapping library	nuID2IlluminaID
Mapping nuID into Illumina ProbeID	nuID2probeID
Map nuID to RefSeq ID	nuID2RefSeqID
Mapping nuID into Illumina TargetID	nuID2targetID
Pair plot of an ExpressionSet object	pairs,ExpressionSet-method pairs-methods pairs.ExpressionSet
Plot of a ExpressionSet object	plot,ExpressionSet,missing-method plot,ExpressionSet-method plot-methods plot.ExpressionSet
plot the cumulative distribution function of a ExpressionSet object	plotCDF plotCDF,ExpressionSet-method plotCDF.ExpressionSet
Plot the color bias density plot of Illumina Infinium Methylation data	plotColorBias1D
Plot the color bias of Illumina Infinium Methylation data in two dimensions	plotColorBias2D
Plot the mean expression (with standard deviation bar) of different type of control probes	plotControlData
plot the density distribution	plotDensity plotDensity.ExpressionSet
plot the fitting results of 'gammaFitEM'	plotGammaFit
Plot the housekeeping gene expression profile	plotHousekeepingGene
visualize the sample relations	plotSampleRelation
plot the Stringency related control probe profiles	plotStringencyGene
plot the VST (Variance Stabilizing Transform) function	plotVST
Mapping Illumina ProbeID as nuID	probeID2nuID
Produce GEO Platform Submission File in SOFT format	produceGEOPlatformFile
Produce the template of GEO sample information	produceGEOSampleInfoTemplate
Produce GEO Sample Submission File in SOFT format	produceGEOSubmissionFile
Produce GEO Sample Submission File of Illumina methylation microarray data in SOFT format	produceMethylationGEOSubmissionFile
Rank Invariant Normalization	rankinvariant
Robust Spline Normalization between chips	rsn
Transfer a nucleotide sequence as a nuID	seq2id
Smooth quantile normalization	smoothQuantileNormalization
Simple Scaling Normalization	ssn
Mapping Illumina TargetID (GeneID) into nuID	targetID2nuID
Variance Stabilizing Transformation	vst

Package: lumi 2.59.0

lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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