This function is useful for loading Illumina methylation data into a [MethyLumiSet-class] object. Sample information can be supplied and will then be incorporated into the resulting phenoData slot.
Arguments
- filename
A filename of the excel-like file from BeadStudio.
- qcfile
A filename of the excel-like QC file from BeadStudio.
- sampleDescriptions
A data.frame that contains at least one column, SampleID (case insensitive). This column MUST match the part of the column headers before the `.Avg_Beta`, etc. Also, if a column called SampleLabel (case insensitive) is present, it is used for sample labels, IF that column contains unique identifiers.
- sep
Separator used in the BeadStudio (or GenomeStudio) output file. If `NULL`, the function estimates it automatically.
- ...
Passed into [utils::read.delim()].
Details
Autodetects the file format, reads the data, makes substitutions of assayData element names for the various formats so that the method accessors will work, maps `sampleDescriptions` appropriately, and returns a `MethyLumiSet` object.
Examples
## Read in sample information
samps <- read.table(system.file("extdata/samples.txt",
package = "methylumi"), sep = "\t", header = TRUE)
## Perform the actual data reading
## This is an example of reading data from an
## Sentrix Array format file (actually two files,
## one for data and one for QC probes)
mldat <- methylumiR(system.file('extdata/exampledata.samples.txt', package = 'methylumi'),
qcfile = system.file('extdata/exampledata.controls.txt', package = "methylumi"),
sampleDescriptions = samps)
mldat
#>
#> Object Information:
#> MethyLumiSet (storageMode: lockedEnvironment)
#> assayData: 1536 features, 10 samples
#> element names: Avg_NBEADS, BEAD_STDERR, betas, methylated, pvals, unmethylated
#> protocolData: none
#> phenoData
#> sampleNames: M_1 M_2 ... F_10 (10 total)
#> varLabels: sampleID SampleLabel Sample Gender
#> varMetadata: labelDescription
#> featureData
#> featureNames: AATK_E63_R AATK_P519_R ... ZP3_P220_F (1536 total)
#> fvarLabels: TargetID ProbeID ... PRODUCT (17 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:
#> Major Operation History:
#> submitted finished
#> 1 2026-10-16 15:00:59.332941 2026-10-16 15:00:59.461562
#> command
#> 1 methylumiR(filename = system.file("extdata/exampledata.samples.txt", package = "methylumi"), qcfile = system.file("extdata/exampledata.controls.txt", package = "methylumi"), sampleDescriptions = samps)