get_phenotype_id_from_transcriptome_id {avidaR}R Documentation

Get phenotype from transcriptome

Description

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

Usage

get_phenotype_id_from_transcriptome_id(
  transcriptome_id,
  seed_id = FALSE,
  phenotype_binary = FALSE,
  triplestore
)

Arguments

transcriptome_id

Integer or 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.

phenotype_binary

Logical value (TRUE/FALSE) to show/hide phenotype in binary notation (FALSE by default).

triplestore

Object of class triplestore_access which manages database access.

Value

Data frame. Columns: "seed_id" (optional), "transcriptome_id", "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"
)

# Single transcriptome
get_phenotype_id_from_transcriptome_id(
  transcriptome_id = 53674,
  triplestore = avidaDB
)

# More than one transcriptome
get_phenotype_id_from_transcriptome_id(
  transcriptome_id = c(53674, 1666099),
  phenotype_binary = TRUE,
  triplestore = avidaDB
)

# At seed_1 and seed_3
get_phenotype_id_from_transcriptome_id(
  transcriptome_id = 53674, seed_id = c(1,3),
  triplestore = avidaDB
)


[Package avidaR version 1.2.0 Index]