get_phenotype_id_from_genome_seq {avidaR}

R Documentation

Get phenotype from genome sequence

Description

Get the phenotype encoded by the instruction sequence constituting the genome of a digital organism for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_phenotype_id_from_genome_seq(
  genome_seq,
  seed_id = FALSE,
  genome_id = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

genome_seq	String of letters or a list of strings.
seed_id	Integer (from 1 to 1000), a vector of integer values, or a logical value. This integer is used for starting the pseudo-random number generator that represents the environment experiencing a digital organism. If a logical value is used, TRUE returns data found in all environments and FALSE (by default) returns only distinct data regardless of the seed.
genome_id	Logical value (TRUE/FALSE) to show/hide genome_id (FALSE by default).
phenotype_binary	Logical value (TRUE/FALSE) to show/hide phenotype_id in binary notation (FALSE by default).
triplestore	Object of class triplestore_access which manages database access.

Value

Data frame. Columns: "seed_id" (optional), "genome_id" (optional), "genome_seq", "phenotype_id", "phenotype_binary" (optional).

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 sequences for genomes_1 and genome_2
sequence1 <- get_genome_seq_from_genome_id(
  genome_id = 1,
  triplestore = avidaDB
)$genome_seq[1]

sequence2 <- get_genome_seq_from_genome_id(
  genome_id = 2,
  triplestore = avidaDB
)$genome_seq[1]

# Single genome
get_phenotype_id_from_genome_seq(
  genome_seq = sequence1,
  triplestore = avidaDB
)

# More than one genome
get_phenotype_id_from_genome_seq(
  genome_seq = c(sequence1, sequence2),
  genome_id = TRUE,
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_phenotype_id_from_genome_seq(
  genome_seq = sequence2,
  seed_id = c(1, 2),
  triplestore = avidaDB
)

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