initREMP {REMP}R Documentation

RE Annotation Database Initialization

Description

initREMP is used to initialize annotation database for RE methylation prediction. Two major RE types in human, Alu element (Alu) and LINE-1 (L1) are available.

Usage

initREMP(arrayType = c("450k", "EPIC"), REtype = c("Alu", "L1"),
  RE = NULL, ncore = NULL, BPPARAM = NULL, export = FALSE,
  work.dir = tempdir(), verbose = FALSE)

Arguments

arrayType

Illumina methylation array type. Currently "450k" and "EPIC" are supported. Default = "450k".

REtype

Type of RE. Currently "Alu" and "L1" are supported.

RE

A GRanges object containing user-specified RE genomic location information. If NULL, the function will retrive RepeatMasker RE database from AnnotationHub (build hg19).

ncore

Number of cores to run parallel computation. By default max number of cores available in the machine will be utilized. If ncore = 1, no parallel computation is allowed.

BPPARAM

An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation. If not specified, default back-end in the machine will be used.

export

Logical. Should the returned REMParcel object be saved to local machine? See Details.

work.dir

Path to the directory where the generated data will be saved. Valid when export = TRUE. If not specified and export = TRUE, temporary directory tempdir() will be used.

verbose

Logical parameter. Should the function be verbose?

Details

Currently, we support two major types of RE in human, Alu and L1. The main purpose of initREMP is to generate and annotate CpG/RE data using the refSeq Gene annotation database (provided by AnnotationHub). These annotation data are crucial to RE methylation prediction in remp. Once generated, the data can be reused in the future (data can be very large). Therefore, we recommend user to save the output from initREMP to the local machine, so that user only need to run this function once as long as there is no change to the RE database. To minimize the size of resulting data file, the generated annotation data are only for REs that contain RE-CpGs with neighboring profiled CpGs. By default, the neighboring CpGs are confined within 1200 bp flanking window. This window size can be modified using remp_options.

Value

An REMParcel object containing data needed for RE methylation prediction.

See Also

See remp for RE methylation prediction.

Examples

data(Alu.demo)
remparcel <- initREMP(arrayType = '450k', REtype = 'Alu', RE = Alu.demo, ncore = 1)
remparcel

# Save the data for later use
saveParcel(remparcel)


[Package REMP version 1.4.1 Index]