get_transcriptome_seq_from_transcriptome_id {avidaR}

Get transcriptome sequence from transcriptome

Description

Get the transcriptome sequence of the transcriptome executed by a digital organism for a list of seeds used for starting the pseudo-random number generator (i.e., a set of environments).

Usage

get_transcriptome_seq_from_transcriptome_id(
  transcriptome_id,
  seed_id = FALSE,
  transcriptome_pos = FALSE,
  genome_seq = 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.

transcriptome_pos

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

genome_seq

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), "transcriptome_id", "transcriptome_seq", "transcriptome_pos" (optional), "genome_seq" (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_transcriptome_seq_from_transcriptome_id(
  transcriptome_id = 53674,
  triplestore = avidaDB
)

# More than one transcriptome at seed_1
get_transcriptome_seq_from_transcriptome_id(
  transcriptome_id = c(53674, 1666099),
  seed_id = 1,
  triplestore = avidaDB
)

# At seed_1 and seed_3
get_transcriptome_seq_from_transcriptome_id(
  transcriptome_id = 2,
  seed_id = c(1, 3),
  transcriptome_pos = TRUE,
  triplestore = avidaDB
)