makeGenomicRatioSetFromMatrix {minfi} | 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.

### See Also

`getGenomicRatioSetFromGEO` is similar but reads data from GEO.

### Examples

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

[Package minfi version 1.34.0 Index]