makeEpiTxDbFromRMBase {EpiTxDb} | R Documentation |
Create a EpiTxDb
object from RMBase v2.0 online resources
Description
makeEpiTxDbFromRMBase
will make use of the RMBase v2.0 online
resources.
Usage
EPITXDB_RMBASE_URL
downloadRMBaseFiles(organism, genome, modtype)
makeEpiTxDbFromRMBase(
organism,
genome,
modtype,
tx = NULL,
sequences = NULL,
metadata = NULL,
reassign.ids = FALSE
)
getRMBaseDataAsGRanges(files)
makeEpiTxDbFromRMBaseFiles(
files,
tx = NULL,
sequences = NULL,
metadata = NULL,
reassign.ids = FALSE
)
listAvailableOrganismsFromRMBase()
listAvailableGenomesFromRMBase(organism)
listAvailableModFromRMBase(organism, genome)
Arguments
organism |
A character value, which must match an organism
descriptor on the RMBase download website.
|
genome |
A character value, which must match a genome
descriptor on the RMBase download website.
|
modtype |
A character value, which must match one or more
modification descriptors on the RMBase download website.
|
tx |
A GRangesList object
which will be used to shift the genomic coordinates to transcript
coordinates. This is optional, but highly recommended. (default:
tx = NULL ).
|
sequences |
A named DNAStringSet or RNAStringSet , which
will be used to check whether the defined modifications are compatible with
the original base. This uses
removeIncompatibleModifications()
function from the Modstrings package.
|
metadata, reassign.ids |
See makeEpiTxDb
|
files |
From organism , genome and modtype the
available files will be downloaded using the
BiocFileCache interface
and passed on to makeEpiTxDbFromRMBaseFiles . However, individual
files can be provided as well.
|
Format
An object of class character
of length 1.
Value
a EpiTxDb
object.
[Package
EpiTxDb version 1.5.0
Index]