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

Description Usage Arguments Format Value Examples

View source: R/tRNAdbImport-import.R

Description

title

Usage

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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

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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.