combo: Combine MethyLumiSet objects

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/combo.R

Description

This is a wrapper for combining different MethyLumiSet objects.

Usage

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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 <[email protected]>

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

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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 Oct. 27, 2018, 3:26 a.m.