readEPIC: readEPIC

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

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 - [e-mail]

References

methylumi

Examples

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

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.