makeGenomicRatioSetFromMatrix: 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.

Value

A GenomicRatioSet object.

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 rownmaes of mat are used to match the 450K array features. Alternatively the rownames can be supplied directly through rownames.

Examples

Run this code

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