findRECpG {REMP}R Documentation

Find RE-CpG genomic location given RE ranges information

Description

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

Usage

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

Arguments

RE.hg19

an GRanges object of RE genomic location database. This can be obtained by fetchRMSK.

REtype

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

be

A BiocParallel object containing back-end information that is ready for paralle computing. This can be obtained by getBackend.

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 'stand' information indicates the strand of the RE.

Value

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

Examples

data(Alu.demo)
be <- getBackend(1, verbose = TRUE)
RE.CpG <- findRECpG(Alu.demo, 'Alu', be, verbose = TRUE) 
RE.CpG


[Package REMP version 1.4.1 Index]