wateRmelon (version 1.16.0)

readEPIC: 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, ...)

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

...

Additional arguments passed to methylumIDAT

Value

A MethyLumiSet object.

Details

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

References

methylumi

Examples

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