makeGenomicRatioSetFromMatrix: Make a GenomicRatioSet from a matrix
In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

makeGenomicRatioSetFromMatrix

R Documentation

Make a GenomicRatioSet from a matrix

Description

Make a GenomicRatioSet from a matrix.

Usage

makeGenomicRatioSetFromMatrix(mat, rownames = NULL, pData = NULL,
                              array = "IlluminaHumanMethylation450k",
                              annotation = .default.450k.annotation,
                              mergeManifest = FALSE, what = c("Beta", "M"))

Arguments

`mat`	The matrix that will be converted.
`rownames`	The feature IDs associated with the rows of `mat` that will be used to match to the IlluminaHumanMethylation450k feature IDs.
`pData`	A `DataFrame` or `data.frame` describing the samples represented by the columns of `mat`. If the rownames of the `pData` don't match the colnames of `mat` these colnames will be changed. If `pData` is not supplied, a minimal `DataFrame` is created.
`array`	Array name.
`annotation`	The feature annotation to be used. This includes the location of features thus depends on genome build.
`mergeManifest`	Should the Manifest be merged to the final object.
`what`	Are `Beta` or `M` values being downloaded.

Details

Many 450K data is provided as csv files. This function permits you to convert a matrix of values into the class that is used by functions such as bumphunter and blockFinder. The rownames of mat are used to match the 450K array features. Alternatively the rownames can be supplied directly through rownames.

Value

A GenomicRatioSet object.

Author(s)

Rafael A. Irizarryrafa@jimmy.harvard.edu.

Examples

mat <- matrix(10,5,2)
rownames(mat) <- c( "cg13869341", "cg14008030","cg12045430", "cg20826792","cg00381604")
grset <- makeGenomicRatioSetFromMatrix(mat)

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.