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DESCEND.control.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deconvSingle.R
\name{DESCEND.control}
\alias{DESCEND.control}
\title{The control parameters of the function \code{\link{runDescend}} and \code{\link{deconvSingle}}}
\usage{
DESCEND.control(n.points = 50, nStart = 2, nStart.lrt = 2,
max.quantile = 0.95, max.sparse = c(0.99, 20), LRT.Z.select = T,
LRT.Z0.select = T, LRT.Z.values = 0, zeroInflate = T,
dense.add.0 = T, only.integer = F, rel.info.range = c(5e-04, 0.01),
rel.info.guide = 0.005, c0.start = 1, aStart = 1, bStart = 0,
gStart = 0, start.sd = 0.2, penalty.Z0 = T, pDegree = 5,
max.c0.iter = 5, c0.min = 1e-05)
}
\arguments{
\item{n.points}{number of discritized points of the underlying true expression distribution. Default is 50}
\item{nStart}{number of random starts for the optimization problem (as it is non-convex) to find the global minimum. Default is 2}
\item{nStart.lrt}{number of random starts for the unpenalized optimization problem for likelihood ratio testing}
\item{max.quantile}{the maximum quantile of the non-zero observed counts used for finding the range of the underlying true expression distribution. Default is 0.98}
\item{max.sparse}{a vector of 2 indicating the maximum sparsity allowed for a gene to be computed. The first element is the fraction of zero-counts allowed, the second element is the minimum number of non-zero counts. Both criteria should be satisfied. Default is (0.95, 25). For studying active fraction, one should increase the threshold to get estimates with acceptable accuracy.}
\item{LRT.Z.select}{a vector of length 1 or the number of columns of \code{Z} indicating for which column of \code{Z} the coefficients are tested against the corresponding value in \code{LRT.Z.values} using LRT. Default is TRUE, meaning that all columns are tested when LRT tests are performed.}
\item{LRT.Z0.select}{a vector of length 1 or the number of columns of \code{Z0} indicating for which column of \code{Z0} the coefficients are tested against 0 using LRT. Default is TRUE, meaning that all columns are tested when LRT tests are performed.}
\item{LRT.Z.values}{a vector of length 1 or the number of columns of \code{Z} showing the values that LRT tests on coefficients of \code{Z} are tested against. Default value is 0, meanings that all tests are tested against 0.}
\item{zeroInflate}{whether to include the zero inflation part to the deconvolved distribution. Default is TRUE}
\item{dense.add.0}{whether smooth the density at 0 into \code{density.points} in the output DESCEND object}
\item{only.integer}{whether set the discrete points to be integers. Default is FALSE}
\item{rel.info.range}{the relative information range allowed for finding the optimal tuning parameter \code{c0}}
\item{rel.info.guide}{one parameter inside the \code{rel.info.range} controling for the searching process of \code{c0}}
\item{c0.start}{the starting value of \code{c0}. Default is 1}
\item{aStart}{the starting values of the spline coefficients of the deconvolved distribution}
\item{bStart}{the starting values of the coefficients of Z0}
\item{gStart}{the starting values of the coefficients of Z}
\item{start.sd}{standard deviation of the random starting values when nStart > 1}
\item{penalty.Z0}{whether add penalty to the coefficients of Z0 or not in optimization. Default is TRUE}
\item{pDegree}{degree of the spline bases. Default is 5}
\item{max.c0.iter}{maximum iteration allowed to find the optimal \code{c0}}
\item{c0.min}{minimum \code{c0} allowed to avoid degeneration}
}
\description{
The control parameters of the function \code{\link{runDescend}} and \code{\link{deconvSingle}}
}