Description Usage Arguments Details Value Examples
findRECpG
is used to obtain RE-CpG genomic location data.
1 2 3 4 5 6 7 |
RE |
A |
REtype |
Type of RE. Currently |
genome |
Character parameter. Specify the build of human genome. Can be either |
be |
A |
verbose |
logical parameter. Should the function be verbose? |
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.
A GRanges
object containing identified RE-CpG genomic
location data.
1 2 3 4 5 6 | data(Alu.hg19.demo)
RE.CpG <- findRECpG(RE = Alu.hg19.demo,
REtype = "Alu",
genome = "hg19",
verbose = TRUE)
RE.CpG
|
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