makeEpiTxDbFromtRNAdb {EpiTxDb} | R Documentation |
EpiTxDb
object from tRNAdb resourcesmakeEpiTxDbFromtRNAdb
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
.
gettRNAdbDataAsGRanges( organism, sequences = NULL, dbURL = tRNAdbImport::TRNA_DB_URL ) makeEpiTxDbFromtRNAdb( organism, sequences = NULL, metadata = NULL, dbURL = tRNAdbImport::TRNA_DB_URL ) listAvailableOrganismsFromtRNAdb()
organism |
A |
sequences |
A named |
dbURL |
The URL to the tRNA db website. |
metadata |
See |
a EpiTxDb
object.
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.
## 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)