Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simple-estimate.R
\name{simpleEstimate}
\alias{simpleEstimate}
\alias{simpleEstimate.SCESet}
\alias{simpleEstimate.matrix}
\title{Estimate simple simulation parameters}
\usage{
simpleEstimate(counts, params = newSimpleParams())
\method{simpleEstimate}{SCESet}(counts, params = newSimpleParams())
\method{simpleEstimate}{matrix}(counts, params = newSimpleParams())
}
\arguments{
\item{counts}{either a counts matrix or an SCESet object containing count
data to estimate parameters from.}
\item{params}{SimpleParams object to store estimated values in.}
}
\value{
SimpleParams object containing the estimated parameters.
}
\description{
Estimate simulation parameters for the simple simulation from a real dataset.
}
\details{
The \code{nGenes} and \code{nCells} parameters are taken from the size of the
input data. The mean parameters are estimated by fitting a gamma distribution
to the library size normalised mean expression level using
\code{\link[fitdistrplus]{fitdist}}. See \code{\link{SimpleParams}} for more
details on the parameters.
}
\examples{
data("sc_example_counts")
params <- simpleEstimate(sc_example_counts)
params
}