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lumi (version 2.24.0)

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

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.

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Version

Version

2.24.0

License

LGPL (>= 2)

Maintainer

Pan Du

Last Published

February 15th, 2017

Functions in lumi (2.24.0)

adjColorBias.quantile

Color bias adjustment of Illumina Infinium methylaton microarrays using smooth quantile normalization

Add the nuID information to the LumiBatch object

Convert methylation M-value to Beta-value

addAnnotationInfo

Add probe color channel and basic annotation information based on the annotation library of Illumina methylation microarray

example.methyTitration

Example Illumina Infinium Methylation titration data in MethyLumiM class

plotColorBias2D

Plot the color bias of Illumina Infinium Methylation data in two dimensions

Estimate methylation M-value matrix

getControlProbe

Get the control probe Ids

plot the density distribution

Pair plot of an ExpressionSet object

plot the fitting results of gammaFitEM

From raw Illumina probe intensities to expression values

Convert methylation Beta-value to M-value

estimateMethylationBG

Estimate the background levels of Illumina Infinium methylaton microarrays

produceGEOSubmissionFile

Produce GEO Sample Submission File in SOFT format

Between chip normalization of a LumiBatch object

Estimate methylation Beta-value matrix

colorBiasSummary

A summary of colorBias information

methylationCall

Estimated methylation call

plotStringencyGene

plot the Stringency related control probe profiles

normalizeMethylation.ssn

Shift and scaling normalization of Illumina Infinium methylation data at probe level

Mapping Illumina TargetID (GeneID) into nuID

plot the cumulative distribution function of a ExpressionSet object

Get the types of the control probes

plotControlData

Plot the mean expression (with standard deviation bar) of different type of control probes

plotHousekeepingGene

Plot the housekeeping gene expression profile

produceGEOPlatformFile

Produce GEO Platform Submission File in SOFT format

Normalize the Illumina Infinium methylation data

adjColorBias.ssn

Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization

MAplot of a ExpressionSet object

Example Illumina Expression data in LumiBatch class

A package for preprocessing Illumina microarray data

Estimate the coefficient of variance matrix of LumiBatch object

Read BeadStudio output files in batch

Estimate the detectable probe ratio

Detect the outlier sample (or gene)

produceMethylationGEOSubmissionFile

Produce GEO Sample Submission File of Illumina methylation microarray data in SOFT format

density-methods

Density plot of a ExpressionSet object

Plot of a ExpressionSet object

boxplot-methods

boxplot of a ExpressionSet object

Get Illumina Chip Information based on probe identifiers

get the chromosome location information of methylation probes

Fitting a curve with monotonic spline

IlluminaID2nuID

Matching Illumina IDs to nuID based on Illumina ID mapping library

Mapping nuID into Illumina ProbeID

smoothQuantileNormalization

Smooth quantile normalization

nuID self-identification

Monotonic smooth method

Mapping Illumina ProbeID as nuID

Map nuID to RefSeq ID

lumiMethyStatus

Estimate the methylation status of individual methylation sites

Reading Illumina methylation microarray data

Transfer a nuID as a nucleotide sequence

asBigMatrix-methods

convert the data matrix in the assayData of a ExpressionSet as BigMatrix

plotSampleRelation

visualize the sample relations

Map nuID to Entrez ID

Rank Invariant Normalization

Density plot of a ExpressionSet object

Transfer a nucleotide sequence as a nuID

bgAdjustMethylation

Estimate and adjust the background levels of Illumina Infinium methylaton microarrays

nuID2IlluminaID

Matching nuIDs to Illumina IDs based on Illumina ID mapping library

plot the VST (Variance Stabilizing Transform) function

importMethyIDAT

Import Illumina methylation .idat files as an MethyLumiM object

example.lumiMethy

Example Illumina Infinium Methylation data in MethyLumiM class

Read in Illumina expression data

Get control probe information

Transfer the Illumina data to stabilize the variance

boxplotColorBias

Plot the Illumina Infinium methylation color bias in terms of boxplot

normalizeMethylation.quantile

Quantile normalization of Illumina Infinium methylation data at probe level

Background adjustment for Illumina data

produceGEOSampleInfoTemplate

Produce the template of GEO sample information

Inverse VST transform

boxplot,MethyLumiM-method

boxplot of a MethyLumiM object

getNuIDMappingInfo

get the mapping information from nuID to RefSeq ID

Estimate the methylation status by fitting a Gamma mixture model using EM algorithm

Background correction of Illumina Expression data

Adjust background level of Illumina Infinium methylation data

estimateIntensity

Estimate intensity of Illumina methylation data

addControlData2lumi

Add the control probe data into the controlData slot of LumiBatch object

addControlData2methyLumiM

Add methylation control data to a MethyLumiM object

LumiBatch-class

Class LumiBatch: contain and describe Illumina microarray data

plotColorBias1D

Plot the color bias density plot of Illumina Infinium Methylation data

Mapping nuID into Illumina TargetID

Color bias adjust of Illumina Infinium methylation data

Variance Stabilizing Transformation

Simple Scaling Normalization

Quality control evaluation of the LumiBatch object

Robust Spline Normalization between chips