import.tRNAdb: Importing information from the tRNA db as GRanges object

In tRNAdbImport: Importing from tRNAdb and mitotRNAdb as GRanges objects

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 httr 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.

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")

tRNAdbImport documentation built on Nov. 8, 2020, 6:50 p.m.