combo: Combine MethyLumiSet objects

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

Combine MethyLumiSet objects

Description

This is a wrapper for combining different MethyLumiSet objects.

Usage

combo(...)

Arguments

...	Eventually, any number of MethyLumiSet objects. Currently only guaranteed for 2 objects.

Details

This is a wrapper for methylumi::combine, which works around a name clash with a different combine function from the gdata package, and also a bug in methylumi::combine.

Value

a MethyLumiSet. The assayData, QCdata, experimentData, protocolData and phenoData are joined on sampleName . featureData and annotation are taken from the object given in the first argument

Note

the function uses sampleNames and gets rid of duplicates. Numeric sampleNames cause problems (and are a Bad Idea anyway). They should be turned into names with make.names() first.

Author(s)

Leo Schalkwyk <[e-mail]>

References

[1] Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)

See Also

as.methylumi

Examples

library(wateRmelon)
data(melon)
## pretend we have two different data sets
melon
pelon <- melon
sampleNames(pelon) <- gsub('^6', 7, sampleNames(pelon))
combo(melon, pelon)

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.