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

Description Usage Arguments Details Value Examples

View source: R/REMPtools.R

Description

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

Usage

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findRECpG(
  RE,
  REtype = c("Alu", "L1", "LTR"),
  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 "LTR" 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

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

REMP documentation built on Nov. 8, 2020, 8:05 p.m.