readEPIC {wateRmelon} | R Documentation

## readEPIC

### Description

Reads Epic arrays from raw idats into `MethyLumiSet` objects from directory.

### Usage

    readEPIC(idatPath, barcodes=NULL, pdat=NULL,parallel=F,n=T,oob=F,force=F, ...)

### Arguments

`idatPath` | Path directory where .idat files are located. `readEPIC` looks in the specified path and converts all .idats within path to relevant barcodes, which is then passed to a modified version of `methylumIDAT` to parse all idats present in the specified directory.
`barcodes` | If NULL, function will search supplied argument in "idatPath" for all idats within directory. If given a vector of barcodes, readEPIC will search for those specific barcodes within the idatPath supplied.
`parallel` | If TRUE, an attempt will be made to process using multiple cores on a multicore machine.
`pdat` | A data.frame describing the samples. A special column named "barcodes" can be used to specify the barcodes to be read when using `methylumIDATepic`. See `methylumIDAT for usage`
`n` | If TRUE, beadcounts from .idats will be included in final object
`oob` | If TRUE, out-of-band (OOB) or opposite-channel signals will be kept
`force` | If TRUE, will combine EPIC IDATs read with differing dmaps
`...` | Additional arguments passed to `methylumIDAT`

### Details

Read a set of .idat files within a file directory and return a `MethylumiSet` object.

### Value

A `MethyLumiSet` object.

### Note

Contains heavily modified version of `methylumIDAT` and other accessory functions used to construct a `MethylumiSet` object, specifically tailored for EPIC arrays. `readEPIC` can also handle 450k and 27k arrays as `methylumIDAT` functionality for these platforms remains unchanged.

Alternatively it is possible to invoke `methylumIDATepic` to use the modified version `methylumIDAT`, which has similar usage.

EPIC manifest has since been updated to B4 version, which has notably fewer probes than previous manifests. It is entirely possible that we will migrate to the manifest packages available on BioConductor and allow for versioning control.

### Author(s)

Tyler Gorrie-Stone - tgorri@essex.ac.uk

### References

methylumi

### Examples

    #Ficticious file pathway
    # path <- "Data/Experiment/Idatlocation"
    # data <- readEPIC(path, barcodes = NULL oob=F, n=T)

[Package wateRmelon version 1.22.1 Index]