get_tandem_id_from_genome_id {avidaR} | R Documentation |
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
)
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. |
Value
Data frame. Columns: "seed_id" (optional), "genome_id", "tandem_id", "tandem_seq" (optional), "tandem_pos" (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 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
)