modifications: Getting modification data from a 'EpiTxDb-object'

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

Getting modification data from a EpiTxDb-object

Description

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.

Usage

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)

Arguments

x	a EpiTxDb
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: columns = c("mod_id","mod_type","mod_name"))
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: filter = NULL)
use.names	TRUE or FALSE. If TRUE, the modification names are set as the names of the returned object. (default: use.names = FALSE)
...	Not used.
by	By which information type should the result be split into? A character value from one of the following values: seqnames mod_type reaction specifier specifier_type
sequences	A RNAStringSet, which can be used as input for combineIntoModstrings(). See ?combineIntoModstrings for additional details.

Value

a GRanges object for modifications and a GRangesList for modificationsBy.

Examples

etdb_file <- system.file("extdata", "EpiTxDb.Hs.hg38.snoRNAdb.sqlite",
                        package="EpiTxDb")
etdb <- loadDb(etdb_file)
etdb

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