sigminer (version 0.1.11)

test_run_components: Test running status for getting components

Description

This is used when user find it is hard to determine component number by get_components function.

Usage

test_run_components(CN_features, feature_name = c("segsize", "bp10MB",
  "osCN", "bpchrarm", "changepoint", "copynumber"), seed = 123456,
  min_comp = 2, max_comp = 10, min_prior = 0.001,
  model_selection = "BIC", nrep = 1, niter = 1000)

Arguments

CN_features

a list generate from get_features() function.

feature_name

feature name to test.

seed

seed number.

min_comp

minimal number of components to fit, default is 2.

max_comp

maximal number of components to fit, default is 10.

min_prior

minimal prior value, default is 0.001. Details about custom setting please refer to flexmix package.

model_selection

model selection strategy, default is 'BIC'. Details about custom setting please refer to flexmix package.

nrep

number of run times for each value of component, keep only the solution with maximum likelihood.

niter

maximal number of iteration to achive converge.

Value

a list contain flexmix object of copy-number features.

Examples

# NOT RUN {
# Load copy number features
load(system.file("extdata", "toy_cn_features.RData",
  package = "sigminer", mustWork = TRUE
))

# Test component number from 2 to 3 for feature 'sigment size'
test_run_components(cn_features, feature_name = "segsize", max_comp = 3)
# }