R/zigControl.R

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

#' Settings for the fitZig function
#'
#' @param tol The tolerance for the difference in negative log likelihood estimates for a feature to remain active.
#' @param maxit The maximum number of iterations for the expectation-maximization algorithm.
#' @param verbose Whether to display iterative step summary statistics or not.
#' @param dfMethod Either 'default' or 'modified' (by responsibilities).
#' @param pvalMethod Either 'default' or 'bootstrap'.
#' @return The value for the tolerance, maximum no. of iterations, and the verbose warning.
#' @note \code{\link{fitZig}} makes use of zigControl.
#'
#' @name zigControl
#' @aliases settings2
#' @seealso \code{\link{fitZig}} \code{\link{cumNorm}} \code{\link{plotOTU}}
#' @examples
#' control =  zigControl(tol=1e-10,maxit=10,verbose=FALSE)
#'
zigControl <-function(tol=1e-4,maxit=10,verbose=TRUE,dfMethod="modified",pvalMethod="default"){
	# to do: add stop if not
	DFMETHODS <- c("default", "modified")
	PMETHODS  <- c("default", "bootstrap")
	dfMethod  <- DFMETHODS[pmatch(dfMethod, DFMETHODS)]
	pvalMethod<- PMETHODS[pmatch(pvalMethod,PMETHODS)]

	stopifnot(dfMethod%in%DFMETHODS)
	stopifnot(pvalMethod%in%PMETHODS)

	set <-list(tol=tol,maxit=maxit,verbose=verbose,dfMethod=dfMethod,pvalMethod=pvalMethod);
	return(set)	
}