Fit Mixture Models for each CN-Feature
FitMixtureModels.Rd
Perform mixture modelling on CN-features using either a mixture of gaussians or poissons.
Usage
FitMixtureModels(
CN_features,
seed = 77777,
min_comp = 2,
max_comp = 10,
min_prior = 0.001,
model_selection = "BIC",
nrep = 1,
niter = 1000,
cores = 1,
featsToFit = seq(1, 6)
)
Arguments
- CN_features
A list. The output from either the ExtractRelativeCopyNumberFeatures or ExtractCopyNumberFeatures functions.
- seed
Integer. (flexmix param) The random seed to use while modelling.
- min_comp
Integer. (flexmix param) The minimum number of components for each CN-feature to consider.
- max_comp
Integer. (flexmix param) The maximum number of components for each CN-feature to consider.
- min_prior
Numeric. (flexmix param) Minimum prior probability of clusters, components falling below this threshold are removed during the iteration.
- model_selection
Integer or character. (flexmix param) Which model to get. Choose by number or name of the information criterion.
- nrep
Integer. (flexmix param) The number of times flexmix is run for each k (number of components).
- niter
Integer. (flexmix param) The maximum number of iterations for the EM-algorithm.
- cores
Integer. The number of cores to use for parallel processing.
- featsToFit
Integer vector. The CN-features to fit.
Details
The segment size, changepoint copy number, and segment copy-number value CN-features are modelled with a mixture of Gaussians. For the breakpoint count per 10MB, length of segments with oscillating copy-number, and breakpoint count per chromosome a mixture of Poissons is used instead. Mixture modelling is done using the FlexMix package.