REMParcel-class: REMParcel instances

In YinanZheng/REMP: Repetitive Element Methylation Prediction

REMParcel instances

Description

REMParcel is a container class to organize required datasets for RE methylation prediction generated from initREMP and used in remp.

Usage

REMParcel(
  REtype = "Unknown",
  genome = "Unknown",
  platform = "Unknown",
  RefGene = GRanges(),
  RE = GRanges(),
  RECpG = GRanges(),
  ILMN = GRanges()
)

getParcelInfo(object)

getRefGene(object)

getRE(object)

getRECpG(object)

getILMN(object, ...)

saveParcel(object, ...)

## S4 method for signature 'REMParcel'
saveParcel(object, work.dir = tempdir(), verbose = FALSE, ...)

## S4 method for signature 'REMParcel'
getParcelInfo(object)

## S4 method for signature 'REMParcel'
getRefGene(object)

## S4 method for signature 'REMParcel'
getRE(object)

## S4 method for signature 'REMParcel'
getRECpG(object)

## S4 method for signature 'REMParcel'
getILMN(object, REonly = FALSE)

Arguments

REtype	Type of RE ("Alu", "L1", or "ERV").
genome	Specify the build of human genome. Can be either "hg19" or "hg38".
platform	Illumina methylation profiling platform ("450k" or "EPIC").
RefGene	refSeq gene annotation data, which can be obtained by fetchRefSeqGene.
RE	Annotated RE genomic range data, which can be obtained by fetchRMSK and annotated by GRannot.
RECpG	Genomic range data of annotated CpG site identified in RE DNA sequence, which can be obtained by findRECpG and annotated by GRannot.
ILMN	Illumina CpG probe genomic range data.
object	A REMParcel object.
...	For saveParcel: other parameters to be passed to the saveRDS method. See saveRDS.
work.dir	For saveParcel: path to the directory where the generated data will be saved. If not specified, temporary directory tempdir() will be used.
verbose	For saveParcel: logical parameter. Should the function be verbose?
REonly	For getILMN: see Accessors.

Value

An object of class REMParcel for the constructor.

Accessors

getParcelInfo(object)

Return data type, RE type, and flanking window size information of the parcel.

getRefGene(object)

Return RefSeq gene annotation data.

getRE(object)

Return RE genomic location data for prediction (annotated by refSeq gene database).

getRECpG(object)

Return RE-CpG genomic location data for prediction.

getILMN(object, REonly = FALSE)

Return Illumina CpG probe genomic location data for prediction (annotated by refSeq gene database). If REonly = TRUE, only probes within RE region are returned.

Utilities

saveParcel(object, work.dir = tempdir(), verbose = FALSE, ...)

Save the object to local machine.

Examples

showClass("REMParcel")

YinanZheng/REMP documentation built on May 14, 2022, 5:58 p.m.