Description Usage Arguments Value Accessors Utilities Examples
REMParcel
is a container class to organize required datasets for
RE methylation prediction generated from initREMP
and used in remp
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | REMParcel(
REtype = "Unknown",
genome = "Unknown",
platform = "Unknown",
RefGene = GRanges(),
RE = GRanges(),
RECpG = GRanges(),
ILMN = GRanges()
)
getParcelInfo(object)
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'
getParcelInfo(object)
## 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 ( |
genome |
Specify the build of human genome. Can be either |
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.
getParcelInfo(object)
Return data type, RE type, and flanking window size information of the parcel.
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.
1 | showClass("REMParcel")
|
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