makeEpiTxDbFromtRNAdb: Create a 'EpiTxDb' object from tRNAdb resources

In FelixErnst/EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface

Create a EpiTxDb object from tRNAdb resources

Description

makeEpiTxDbFromtRNAdb will make use of the tRNAdb online resources and extract the modification information from the RNA database.

If a named DNAStringSet is provided as sequences, the result from the tRNAdb will be matched against the sequences. Valid matches will be used as transcript identifiers and returned after a check of modification compatibility with the provided sequence. By this process multiple copies of transcripts can be associated with a single modification.

makeEpiTxDbFromtRNAdb uses the functions provided by the tRNAdbImport package. import.tRNAdb will be used with database = "RNA" and the three different values for origin.

Usage

gettRNAdbDataAsGRanges(
  organism,
  sequences = NULL,
  dbURL = tRNAdbImport::TRNA_DB_URL
)

makeEpiTxDbFromtRNAdb(
  organism,
  sequences = NULL,
  metadata = NULL,
  dbURL = tRNAdbImport::TRNA_DB_URL
)

listAvailableOrganismsFromtRNAdb()

Arguments

organism	A character value for an organism available on the tRNAdb website.
sequences	A named DNAStringSet or RNAStringSet, which will be used to associate a tRNAdb result with a specific transcript.
dbURL	The URL to the tRNA db website.
metadata	See makeEpiTxDb

Value

a EpiTxDb object.

References

Juehling F, Moerl M, Hartmann RK, Sprinzl M, Stadler PF, Puetz J. 2009. "tRNAdb 2009: compilation of tRNA sequences and tRNA genes." Nucleic Acids Research, Volume 37 (suppl_1): D159–162. doi:10.1093/nar/gkn772.

Examples

## Not run: 
# getting just the annotation data
etdb <- makeEpiTxDbFromtRNAdb("Saccharomyces cerevisiae")

# For associating the result with transcripts, provide and additional
# named DNAStringSet object. Matching will be done against each sequence
# allowing 5 mismatches and indels. The final result will be checked for
# validity regarding the identity of the modifications
etdb <- makeEpiTxDbFromtRNAdb("Saccharomyces cerevisiae",
                              some_transcript_sequences)

## End(Not run)

FelixErnst/EpiTxDb documentation built on March 31, 2024, 1:21 a.m.