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Luke Zappia authored
* master: (50 commits) Run checks and bump version Add ZINB-WaVE simulation to lists Convert mfaSimulate output to counts Convert phenoSimulate output to counts Add zinbEstimate Add zinbSimulate Adjust ZINBParams defaults Add ZINBParams tests Add ZINBParams Add pheno to lists Add phenoEstimate Add phenoSimulate Add PhenoParams Fix quotes bug in tests Bump version Add mfa tests Run checks Add mfa to lists Add mfaSimulate Add mfaEstimate ...
Luke Zappia authored* master: (50 commits) Run checks and bump version Add ZINB-WaVE simulation to lists Convert mfaSimulate output to counts Convert phenoSimulate output to counts Add zinbEstimate Add zinbSimulate Adjust ZINBParams defaults Add ZINBParams tests Add ZINBParams Add pheno to lists Add phenoEstimate Add phenoSimulate Add PhenoParams Fix quotes bug in tests Bump version Add mfa tests Run checks Add mfa to lists Add mfaSimulate Add mfaEstimate ...
MFAParams.Rd 1.26 KiB
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllClasses.R
\docType{class}
\name{MFAParams}
\alias{MFAParams}
\alias{MFAParams-class}
\title{The MFAParams class}
\description{
S4 class that holds parameters for the mfa simulation.
}
\section{Parameters}{
The mfa simulation uses the following parameters:
\describe{
\item{\code{nGenes}}{The number of genes to simulate.}
\item{\code{nCells}}{The number of cells to simulate.}
\item{\code{[seed]}}{Seed to use for generating random numbers.}
\item{\code{[trans.prop]}}{Proportion of genes that show transient
expression. These genes are briefly up or down-regulated before returning
to their initial state}
\item{\code{[zero.neg]}}{Logical. Whether to set negative expression
values to zero. This will zero-inflate the data.}
\item{\code{[dropout.present]}}{Logical. Whether to simulate dropout.}
\item{\code{dropout.lambda}}{Lambda parameter for the exponential
dropout function.}
}
The parameters not shown in brackets can be estimated from real data using
\code{\link{mfaEstimate}}. See \code{\link[mfa]{create_synthetic}} for more
details about the parameters. For details of the Splatter implementation of
the mfa simulation see \code{\link{mfaSimulate}}.
}