avidaR (version 1.2.1)

get_tandem_id_from_genome_id: Get tandem repeat from genome

Description

Get the tandem repeat contained in the transcriptome of a digital organism having a specific genome.

Usage

get_tandem_id_from_genome_id(
  genome_id,
  seed_id = FALSE,
  tandem_seq = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Value

Data frame. Columns: "seed_id" (optional), "genome_id", "tandem_id", "tandem_seq" (optional), "tandem_pos" (optional).

Arguments

genome_id

Integer or a list of integer values.

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.

tandem_seq

Logical value (TRUE/FALSE) to show/hide this column (FALSE by default).

tandem_pos

Logical value (TRUE/FALSE) to show/hide this column (FALSE by default).

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"
)

# Single genome
get_tandem_id_from_genome_id(genome_id = 1, triplestore = avidaDB)

# More than one genome
get_tandem_id_from_genome_id(
  genome_id = c(1, 2, 3),
  tandem_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1, seed_3 and seed_5
get_tandem_id_from_genome_id(
  genome_id = 2,
  seed_id = c(1, 3, 5),
  tandem_pos = TRUE,
  triplestore = avidaDB
)