avidaR (version 1.2.1)

get_tandem_id_from_genome_seq: Get tandem repeat from genome sequence

Description

Get the tandem repeat contained in the transcriptome of a digital organism having a specific linear string of letters representing the instruction codes that make up its genome.

Usage

get_tandem_id_from_genome_seq(
  genome_seq,
  seed_id = FALSE,
  tandem_seq = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Value

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

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.

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"
)

# Get sequences for genomes 1 and 2
sequence1 <- get_genome_seq_from_genome_id(
  1,
  triplestore = avidaDB
)$genome_seq

sequence2 <- get_genome_seq_from_genome_id(
  2,
  triplestore = avidaDB
)$genome_seq

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

# More than one genome
get_tandem_id_from_genome_seq(
  genome_seq = c(sequence1, sequence2),
  tandem_seq = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_2
get_tandem_id_from_genome_seq(
  genome_seq = sequence2,
  seed_id = c(1,2),
  tandem_seq = TRUE,
  tandem_pos = TRUE,
  triplestore = avidaDB
)