get_tandem_seq_from_tandem_id {avidaR}

Get the tandem repeat sequence from tandem repeat

Description

Get the tandem sequence from the tandem repeat contained in the transcriptome 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_tandem_seq_from_tandem_id(
  tandem_id,
  seed_id = FALSE,
  genome_id = FALSE,
  tandem_pos = FALSE,
  triplestore
)

Arguments

tandem_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.

genome_id

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.

Value

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

# Single tandem
get_tandem_seq_from_tandem_id(
  tandem_id = 6336945,
  triplestore = avidaDB
)

# More than one tandem at seed_1
get_tandem_seq_from_tandem_id(
  tandem_id = c(6336945, 2520963, 2520963),
  seed_id = 1,
  triplestore = avidaDB
)

# At seed_3 and seed_5
get_tandem_seq_from_tandem_id(
  tandem_id = 6336945,
  seed_id = c(1, 3),
  tandem_pos = TRUE,
  genome_id = TRUE,
  triplestore = avidaDB
)