modifications {EpiTxDb} | R Documentation |
EpiTxDb-object
modifications
and modificationsBy
are functions to
extract modification annotation from a EpiTxDb
object.
modifiedSeqsByTranscript
returns a
ModRNAStringSet
from a EpiTxDb
object and compatible RNAStringSet
object. This used the
combineIntoModstrings()
function from the
Modstrings
package.
modifications( x, columns = c("mod_id", "mod_type", "mod_name"), filter = NULL, use.names = FALSE, ... ) modificationsBy( x, by = c("seqnames", "mod_type", "reaction", "specifier", "specifier_type"), ... ) modifiedSeqsByTranscript(x, sequences, ...) ## S4 method for signature 'EpiTxDb' modifications( x, columns = c("mod_id", "mod_type", "mod_name"), filter = NULL, use.names = FALSE ) ## S4 method for signature 'EpiTxDb' modificationsBy( x, by = c("seqnames", "modtype", "reaction", "specifier", "specifiertype") ) ## S4 method for signature 'EpiTxDb,DNAStringSet' modifiedSeqsByTranscript(x, sequences)
x |
a |
columns |
Columns to include in the result. If the vector is named,
those names are used for the corresponding column in the element metadata
of the returned object. (default: |
filter |
Either NULL or a named list of vectors to be used to restrict
the output. Valid names for this list are: "mod_id", "mod_type",
"mod_name", "sn_id", "sn_name", "rx_genename", "rx_ensembl",
"rx_ensembltrans", "rx_entrezid", "spec_genename", "spec_type",
"spec_ensembl", "spec_ensembltrans", "spec_entrezid" , "ref_type" and
"ref". (default: |
use.names |
|
... |
Not used. |
by |
By which information type should the result be split into? A
|
sequences |
A |
a GRanges
object for
modifications
and a
GRangesList
for
modificationsBy
.
etdb_file <- system.file("extdata", "EpiTxDb.Hs.hg38.snoRNAdb.sqlite", package="EpiTxDb") etdb <- loadDb(etdb_file) etdb