findRECpG: Find RE-CpG genomic location given RE ranges information

In YinanZheng/REMP: Repetitive Element Methylation Prediction

Find RE-CpG genomic location given RE ranges information

Description

findRECpG is used to obtain RE-CpG genomic location data.

Usage

findRECpG(
  RE,
  REtype = c("Alu", "L1", "ERV"),
  genome = c("hg19", "hg38"),
  be = NULL,
  verbose = FALSE
)

Arguments

RE	A GRanges object of RE genomic location database. This can be obtained by fetchRMSK.
REtype	Type of RE. Currently "Alu", "L1", and "ERV" are supported.
genome	Character parameter. Specify the build of human genome. Can be either "hg19" or "hg38". User should make sure the genome build of RE is consistent with this parameter.
be	A BiocParallel object containing back-end information that is ready for parallel computing. This can be obtained by getBackend. If not specified, non-parallel mode is used.
verbose	logical parameter. Should the function be verbose?

Details

CpG site is defined as 5'-C-p-G-3'. It is reasonable to assume that the methylation status across all CpG/CpG dyads are concordant. Maintenance methyltransferase exhibits a preference for hemimethylated CpG/CpG dyads (methylated on one strand only). As a result, methyaltion status of CpG sites in both forward and reverse strands are usually consistent. Therefore, to accommodate the cytosine loci in both strands, the returned genomic ranges cover the 'CG' sequence with width of 2. The 'strand' information indicates the strand of the RE. Locating CpG sites in RE sequences can be computation intensive. It is recommanded to get more than one work in the backend for a faster running speed.

Value

A GRanges object containing identified RE-CpG genomic location data.

Examples

data(Alu.hg19.demo)
RE.CpG <- findRECpG(RE = Alu.hg19.demo, 
                    REtype = "Alu", 
                    genome = "hg19", 
                    verbose = TRUE)
RE.CpG

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