minfi_to_GEO: minfi_to_GEO
In ND91/ndlib: A list of handy functions

Description Usage Arguments Value Author(s) Examples

View source: R/minfi_to_GEO.R

Provide a GEO submission for Illumina methylation data according to the template provided with GPL16304

1	minfi_to_GEO(values, detP, unmeth, meth)

`values`	A matrix or dataframe containing the methylation values (i.e. Beta or M-values)
`detP`	A matrix containing the detection P values per probe
`unmeth`	A matrix containing the unmethylated values per probe with the appropriate row names
`meth`	A matrix containing the methylated values per probe with the appropriate column names

A list of two dataframes: 1) The unmethylated, methylated and detection P-value per sample per probe, and 2) The degree of methylation (Beta, M-value) and the detection P-value per sample per probe.

Andrew Y.F. Li Yim

#"I generally provide GEO the processed beta/M-values, and the unprocessed methylated and unmethylated channels as unprocessed data. The detection P-values should be the same regardless of processing"

#Load data
require(minfiData)
baseDir <- system.file("extdata", package = "minfiData")
targets <- read.metharray.sheet(base = baseDir)
RGset <- read.metharray.exp(targets = targets, recursive = T)

#Preprocess it raw to get the raw methylated and unmethylated channels
Mset.raw <- preprocessRaw(RGset)
meth.raw <- getMeth(Mset.raw)
unmeth.raw <- getUnmeth(Mset.raw)
detP.raw <- detectionP(RGset)

#Preprocess it using your normalization tool of interest
Mset <- preprocessIllumina(rgSet = RGset, bg.correct = T, normalize = "controls", reference = 2)
Rset <- ratioConvert(Mset)
GMset <- mapToGenome(Rset)

#Beta values
Beta.processed <- getBeta(GMset)

geo.submission <- minfi_to_GEO(Beta.processed, detP.raw, unmeth.raw, meth.raw)