read.metharray.exp: Reads an entire metharray experiment using a sample sheet

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

Reads an entire metharray experiment using a sample sheet

Description

Reads an entire methylation array experiment using a sample sheet or (optionally) a target like data.frame.

Usage

read.metharray.exp(base = NULL, targets = NULL, extended = FALSE,
    recursive = FALSE, verbose = FALSE, force = FALSE)

Arguments

base	The base directory.
targets	A targets data.frame, see details
extended	Should the output of the function be a "RGChannelSetExtended" (default is "RGChannelSet").
recursive	Should the search be recursive (see details)
verbose	Should the function be verbose?
force	Should reading different size IDAT files be forced? See the documentation for read.metharray

Details

If the targets argument is NULL, the function finds all two-color IDAT files in the directory given by base. If recursive is TRUE, the function searches base and all subdirectories. A two-color IDAT files are pair of files with names ending in _Red.idat or _Grn.idat.

If the targets argument is not NULL it is assumed it has a columned named Basename, and this is assumed to be pointing to the base name of a two color IDAT file, ie. a name that can be made into a real IDAT file by appending either _Red.idat or _Grn.idat.

The type of methylation array is guess by looking at the number of probes in the IDAT files.

Value

An object of class "RGChannelSet" or "RGChannelSetExtended".

Author(s)

Kasper Daniel Hansen [e-mail].

See Also

read.metharray for the workhorse function, read.metharray.sheet for reading a sample sheet and RGChannelSet for the output class.

Examples

if(require(minfiData)) {

baseDir <- system.file("extdata", package = "minfiData")
RGset <- read.metharray.exp(file.path(baseDir, "5723646052"))

}

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