Create a EpiTxDb object from RMBase v2.0 online resources

makeEpiTxDbFromRMBase will make use of the RMBase v2.0 online resources.

EPITXDB_RMBASE_URL

downloadRMBaseFiles(organism, genome, modtype)

makeEpiTxDbFromRMBase(
  organism,
  genome,
  modtype,
  tx = NULL,
  sequences = NULL,
  metadata = NULL,
  reassign.ids = FALSE,
  verbose = FALSE
)

getRMBaseDataAsGRanges(files, verbose = FALSE)

makeEpiTxDbFromRMBaseFiles(
  files,
  tx = NULL,
  sequences = NULL,
  metadata = NULL,
  reassign.ids = FALSE,
  verbose = FALSE
)

listAvailableOrganismsFromRMBase()

listAvailableGenomesFromRMBase(organism)

listAvailableModFromRMBase(organism, genome)

Format

An object of class character of length 1.

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

verbose

TRUE or FALSE: Should verbose message be prined?

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.

Value

a EpiTxDb object.