cv.emeth: cv.emeth: cross validation for emeth.

In Hanyuz1996/EMeth: Cell type decomposition based on methylation data

Description

An implementation of cross validation for the ridge penalty parameter in EMeth.

Usage

cv.emeth(Y, eta, mu, aber, V, init = "default", nu, family = "laplace", folds = 5, usesubset = TRUE, maxiter = 50, verbose = FALSE)

Arguments

Y	Matrix of size K*I. Methylation of bulk sample for which the cell type decomposition is to be estimated. Y is usually a K*I matrix where K is the number of probes used and I is the number of samples.
eta	Vector of size I. Tumor purity of each sample.
mu	Matrix of size K*Q. Reference matrix, provided by literature. A sample reference data of immune cells is provided in the example directory.
aber	Logic variable: if there is unknown aberrant cell type.
V	string: default to be 'c' which stands for constant weight for all probes. It might be 'b' for binomial variance structure or 'w' for specific weight structure of variance.
init	If init is a string 'default', we will adopt the default random initialization of all parameters for the algorithm. Otherwise one can provide a list of initialization of parameters.
family	string: accept 'normal' or 'laplace' to specify what likelihood will be used in the algorithm.
nu	nonnegative numbers that stand for the penalties, and the opitmal penalty value will be chosen by cross-validation.
folds	Specify the number of folds for the cross validation.
usesubset	Logic variable, if it is true, a random sampled subset of all probes are used to perform cross-validation.
maxiter	max time of iteration of the EM algorithm, default to be 50.
verbose	logic variable. If TRUE then will print additional information in iteration of EMeth.

Value

result	The result of EMeth algorithm using the penalty value selected by cross-validation. It is a list and documentation of its entries can be found in the help file for function emeth
choosenu	The chosen value of nu, the penalty.
losslist	A matrix saving the loss for each fold and each choice of nu.

Author(s)

Hanyu Zhang

Examples

## See examples folder.

Hanyuz1996/EMeth documentation built on Dec. 31, 2020, 12:59 p.m.