MAP_parameters {BCT}

Parameters of the MAP model

Description

Returns the parameters of each leaf contained in the MAP model.

Usage

MAP_parameters(input_data, depth, beta = NULL)

Arguments

input_data

the sequence to be analysed. The sequence needs to be a "character" object. See the examples section of BCT/kBCT functions on how to transform any dataset to a "character" object.

depth

maximum memory length.

beta

hyper-parameter of the model prior. Takes values between 0 and 1. If not initialised in the call function, the default value is 1-2^-m+1, where m is the size of the alphabet; for more information see Kontoyiannis et al. (2020).

Value

list of parameters for each of the context within the MAP model.

See Also

BCT, kBCT, generate_data

Examples

# Use the gene_s dataset:
q <- BCT(gene_s, 10)
expected_contexts <- q[['Contexts']]
expected_contexts
# [1] "3"  "1"  "0"  "23" "20" "21" "22"

# For default beta:
v <- MAP_parameters(gene_s, 10)

# For custom beta (e.g. 0.8):
MAP_parameters(gene_s, 10, 0.8)

# generate a sequence of data using the generate_data function
s <- generate_data(v, 20000)

# Use BCT:
r <- BCT(s, 10)

# Check the resulting contexts:
r[['Contexts']]
# [1] "3"  "0"  "1"  "20" "22" "23" "21"

# The resulting contexts are as expected