lumiMethyR: Reading Illumina methylation microarray data

Description Usage Arguments Details Value Author(s) See Also

View source: R/methylation_preprocessing.R

Description

This function is a wrap of methylumiR function in methylumi package.

Usage

1
lumiMethyR(filename, lib=NULL, controlData=NULL, qcfile=NULL, sampleDescriptions=NULL, sep = NULL)

Arguments

filename

file name output by GenomeStudio

lib

Annotation library of Illumina methylation microarray

controlData

the controlData file name or a MethyLumiQC object to be added to the "controlData" slot of the MethyLumiM object

qcfile

parameter of methylumiR function

sampleDescriptions

parameter of methylumiR function

sep

parameter of methylumiR function

Details

This function is a wrap of methylumiR function in methylumi package. It will coerce the returned object as MethyLumiM class. The methylated and unmethylated probe intensity information is required for color-bias adjustment and normalization. If users have the Illumina IDAT files, we suggest use importMethyIDAT function to import the data. The importMethyIDAT function will automatically retrieve the required information and return a MethyLumiM object.

Value

return a MethyLumiM object

Author(s)

Pan Du

See Also

See Also importMethyIDAT, methylumiR and addControlData2methyLumiM


lumi documentation built on Nov. 8, 2020, 5:27 p.m.

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