import.tRNAdb: Importing information from the tRNA db as GRanges object
In FelixErnst/tRNAdbImport: Importing from tRNAdb and mitotRNAdb as GRanges objects

View source: R/tRNAdbImport-import.R

import.tRNAdb

R Documentation

Importing information from the tRNA db as GRanges object

Description

title

Usage

TRNA_DB_URL

TRNA_DB_URL_MT

import.tRNAdb.id(
  tdbID,
  database = c("DNA", "RNA"),
  origin = c("allothers", "plastid", "mitochondrial"),
  dbURL = TRNA_DB_URL,
  verbose = FALSE
)

import.mttRNAdb.id(mtdbID, dbURL = TRNA_DB_URL_MT, verbose = FALSE)

import.tRNAdb.blast(
  blastSeq,
  database = c("DNA", "RNA"),
  origin = c("allothers", "plastid", "mitochondrial"),
  dbURL = TRNA_DB_URL,
  verbose = FALSE
)

import.tRNAdb(
  organism = "",
  strain = "",
  taxonomyID = "",
  aminoacids = "",
  anticodons = "",
  sequences = list(),
  structures = list(),
  reference = "",
  comment = "",
  pubmed = "",
  genes = "",
  database = c("DNA", "RNA"),
  origin = c("allothers", "plastid", "mitochondrial"),
  dbURL = TRNA_DB_URL,
  verbose = FALSE
)

import.mttRNAdb(
  organism = "",
  strain = "",
  taxonomyID = "",
  aminoacids = "",
  anticodons = "",
  sequences = list(),
  structures = list(),
  reference = "",
  comment = "",
  pubmed = "",
  genes = "",
  dbURL = TRNA_DB_URL_MT,
  verbose = FALSE
)

tRNAdb2GFF(input)

Arguments

`tdbID`	a tRNAdb ID
`database`	"RNA" or "DNA"
`origin`	one ore more of "plastid", "mitochondrial" or "allothers"
`dbURL`	the URL of the tRNA db
`verbose`	whether to report verbose information from the httr2 calls
`mtdbID`	a mtRNAdb ID
`blastSeq`	a sequence to use for a blast search
`organism`	a organism name as a character string
`strain`	a strain information as a character string
`taxonomyID`	organism and strain information as a taxonom ID
`aminoacids`	a character vector of amino acids as a three letter code
`anticodons`	a character vector of anticodon sequences
`sequences`	a named (1-15) list of sequences, which are used for the search
`structures`	a named (1-15) list of structures, which are used for the search. Please use the `\(\)` or `><` dot bracket annotation.
`reference`	a reference as a character string
`comment`	a comment as a character string
`pubmed`	a pubmed ID
`genes`	a gene name as a character string
`input`	a GRanges object which passes the `istRNAdbGRanges` check

Format

An object of class character of length 1.

Value

a GRanges object containing the information from the tRNA db

Examples

import.tRNAdb(organism = "Saccharomyces cerevisiae",
              aminoacids = c("Phe","Ala"))
import.tRNAdb.id(tdbID = "tdbD00000785")
import.tRNAdb.blast(blastSeq =
"GCGGATTTAGCTCAGTTGGGAGAGCGCCAGACTGAAGATCTGGAGGTCCTGTGTTCGATCCACAGAATTCGCA")
import.mttRNAdb(organism = "Bos taurus",
                aminoacids = c("Phe","Ala"))
import.mttRNAdb.id(mtdbID = "mtdbD00000900")

FelixErnst/tRNAdbImport documentation built on April 1, 2024, 2:40 p.m.