initREMP {REMP} | R Documentation |
initREMP
is used to initialize annotation database for RE methylation prediction.
Two major RE types in human, Alu element (Alu) and LINE-1 (L1) are available.
initREMP(arrayType = c("450k", "EPIC"), REtype = c("Alu", "L1"), RE = NULL, ncore = NULL, BPPARAM = NULL, export = FALSE, work.dir = tempdir(), verbose = FALSE)
arrayType |
Illumina methylation array type. Currently |
REtype |
Type of RE. Currently |
RE |
A |
ncore |
Number of cores to run parallel computation. By default max number of cores
available in the machine will be utilized. If |
BPPARAM |
An optional |
export |
Logical. Should the returned |
work.dir |
Path to the directory where the generated data will be saved. Valid when
|
verbose |
Logical parameter. Should the function be verbose? |
Currently, we support two major types of RE in human, Alu and L1. The main purpose of
initREMP
is to generate and annotate CpG/RE data using the refSeq Gene
annotation database (provided by AnnotationHub
). These annotation data are crucial to
RE methylation prediction in remp
. Once generated, the data can be reused in the future
(data can be very large). Therefore, we recommend user to save the output from
initREMP
to the local machine, so that user only need to run this function once
as long as there is no change to the RE database. To minimize the size of resulting data file, the generated
annotation data are only for REs that contain RE-CpGs with neighboring profiled CpGs. By default, the
neighboring CpGs are confined within 1200 bp flanking window. This window size can be modified using
remp_options
.
An REMParcel
object containing data needed for RE methylation prediction.
See remp
for RE methylation prediction.
data(Alu.demo) remparcel <- initREMP(arrayType = '450k', REtype = 'Alu', RE = Alu.demo, ncore = 1) remparcel # Save the data for later use saveParcel(remparcel)