REMParcel-class {REMP} | R Documentation |
REMParcel
is a container class to organize required datasets for
RE methylation prediction generated from initREMP
and used in remp
.
REMParcel(REtype = "Unknown", platform = "Unknown", RefGene = GRanges(), RE = GRanges(), RECpG = GRanges(), ILMN = GRanges()) getRefGene(object) getRE(object) getRECpG(object) getILMN(object, ...) saveParcel(object, ...) ## S4 method for signature 'REMParcel' saveParcel(object, work.dir = tempdir(), verbose = FALSE, ...) ## S4 method for signature 'REMParcel' getRefGene(object) ## S4 method for signature 'REMParcel' getRE(object) ## S4 method for signature 'REMParcel' getRECpG(object) ## S4 method for signature 'REMParcel' getILMN(object, REonly = FALSE)
REtype |
Type of RE ( |
platform |
Illumina methylation profiling platform ( |
RefGene |
refSeq gene annotation data, which can be obtained by |
RE |
Annotated RE genomic range data, which can be obtained by |
RECpG |
Genomic range data of annotated CpG site identified in RE DNA sequence, which can
be obtained by |
ILMN |
Illumina CpG probe genomic range data. |
object |
A |
... |
For |
work.dir |
For |
verbose |
For |
REonly |
For |
An object of class REMParcel
for the constructor.
getRefGene(object)
Return RefSeq gene annotation data.
getRE(object)
Return RE genomic location data for prediction (annotated by refSeq gene database).
getRECpG(object)
Return RE-CpG genomic location data for prediction.
getILMN(object, REonly = FALSE)
Return Illumina CpG probe genomic
location data for prediction (annotated by refSeq gene database). If
REonly = TRUE
, only probes within RE region are returned.
saveParcel(object, work.dir = tempdir(), verbose = FALSE, ...)
Save the object to local machine.
showClass("REMParcel")