mpgex_cluster: Cluster similar methylation profiles

Description Usage Arguments Examples

View source: R/mpgex_cluster.R

Description

mpgex_cluster is a wrapper function that clusters similar methylation profiles using the EM algorithm. Initially, it performs parameter checking, and initializes main parameters, such as mixing proportions, basis function coefficients, then the EM algorithm is applied and finally model selection metrics are calculated, such as BIC and AIC.

Usage

1
2
3
4
mpgex_cluster(x, K = 3, pi_k = NULL, w = NULL, basis = NULL,
  em_max_iter = 100, epsilon_conv = 1e-04, opt_method = "CG",
  opt_itnmax = 100, init_opt_itnmax = 100, is_parallel = TRUE,
  no_cores = NULL, is_verbose = FALSE)

Arguments

x

A list of elements of length N, where each element is an L x 3 matrix of observations, where 1st column contains the locations. The 2nd and 3rd columns contain the total trials and number of successes at the corresponding locations, repsectively.

K

Integer denoting the number of clusters K.

pi_k

Vector of length K, denoting the mixing proportions.

w

A MxK matrix, where each column contains the basis function coefficients for the corresponding cluster.

basis

A 'basis' object. E.g. see polynomial.object

em_max_iter

Integer denoting the maximum number of EM iterations.

epsilon_conv

Numeric denoting the convergence parameter for EM.

opt_method

The optimization method to be used. See optim for possible methods. Default is 'CG'.

opt_itnmax

Optional argument giving the maximum number of iterations for the corresponding method. See optim for details.

init_opt_itnmax

Optimization iterations for obtaining the initial EM parameter values.

is_parallel

Logical, indicating if code should be run in parallel.

no_cores

Number of cores to be used, default is max_no_cores - 1.

is_verbose

Logical, print results during EM iterations

Examples

1
2
3
ex_data <- bpr_data
mpgex_clust <- mpgex_cluster(x = ex_data, em_max_iter = 2, is_parallel = FALSE,
                             opt_itnmax = 5)

andreaskapou/mpgex documentation built on Nov. 25, 2017, 8:08 a.m.