avidaR (version 1.2.1)

get_mutant_at_pos: Get single-point mutants of wild-type organisms

Description

Get the genome sequence of a digital organism (i.e., wild-type) and its single-point mutants.

Usage

get_mutant_at_pos(
  genome_id = NULL,
  inst_replaced = NULL,
  inst_replaced_by = NULL,
  pos = NULL,
  triplestore
)

Value

Data frame: Columns: "genome_id_wild_type", "genome_seq_wild_type", "genome_id_mutant", genome_seq_mutant", "pos".

Arguments

genome_id

Integer or a list of integer values. If not specified, the function will return the single-point mutants of a randomly chosen wild-type organism.

inst_replaced

A letter representing the instruction of the genome sequence of the wild-type organism to be mutated. If not specified, the function will return the single-point mutants that have replaced the letter that the genome of the wild-type organism carried at that position (if the position is specified, otherwise it will return the mutations located on all positions) by the letter indicated in the argument inst_replaced_by (if specified, otherwise it will return all the mutants at that position on the genome of the wild type organism).

inst_replaced_by

A letter representing the instruction of the genome of the single-point mutant that have replaced the instruction of the genome of the wild-type organism. If not specified, the function will return all single-point mutants that have replaced the letter indicated in the argument inst_replaced (if specified, otherwise it will return all the mutants at that position on the genome of the wild type organism) of the genome of the wild-type organism at that position (if the position is specified, otherwise it will return the mutations located on all positions).

pos

Integer representing the position of the single-point mutation along the genome of a digital organism (from 1 to 100 for a genome length of 100 instructions). If not specified, the function will return all single-point mutants of the genome of the wild-type organism.

triplestore

Object of class triplestore_access which manages database access.

Examples

# Create triplestore object
avidaDB <- triplestore_access$new()

# Set access options
avidaDB$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)

get_mutant_at_pos(
  genome_id = 582,
  inst_replaced = 'o',
  inst_replaced_by = 'a',
  pos = 1,
  triplestore = avidaDB)