View source: R/create_alignment_params.R
create_test_alignment_params | R Documentation |
Create testing parameters for the alignment simulation.
create_test_alignment_params(
sim_tral_fun = pirouette::sim_tral_with_std_nsm,
root_sequence = "acgt",
rng_seed = 0,
fasta_filename = pirouette::get_temp_fasta_filename()
)
sim_tral_fun |
function to simulate a
true alignment with.
This function must have two arguments,
called Use check_sim_tral_fun to verify if the function has the right signature and output. Some standard functions:
|
root_sequence |
the DNA sequence at the root of the phylogeny. By default, this will consist out of an equal amount of each letter Use check_root_sequence to check if a root sequence is valid. |
rng_seed |
a random number generator seed |
fasta_filename |
name of a FASTA file. Use get_alignment_id to get the ID of the alignment |
a list of alignment parameters alignment_params <- create_test_alignment_params() check_alignment_params(alignment_params)
Richèl J.C. Bilderbeek
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