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adjacency: Revert to density estimate

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This reverts commit 23bb499d3a.
This commit is contained in:
Elias Projahn 2022-01-13 18:35:02 +01:00
parent 0087f83247
commit 8cda3e8e83
4 changed files with 50 additions and 4 deletions
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4
man/adjacency.Rd
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@ -4,11 +4,11 @@
\alias{adjacency}
\title{Score genes based on their proximity to the reference genes.}
\usage{
adjacency(estimate = stats::median, combination = min)
adjacency(estimate = densest, combination = min)
}
\arguments{
\item{estimate}{A function that will be used to summarize the distance
values for each gene. By default, \code{\link[=median]{median()}} is used.}
values for each gene. See \code{\link[=densest]{densest()}} for the default implementation.}
\item{combination}{A function that will be used to combine the different
distances to the reference genes. By default \code{\link[=min]{min()}} is used. That means

21
man/densest.Rd Normal file
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@ -0,0 +1,21 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/adjacency.R
\name{densest}
\alias{densest}
\title{Find the densest value in the data.}
\usage{
densest(data)
}
\arguments{
\item{data}{The input data.}
}
\value{
The densest value of data.
}
\description{
This function assumes that data represents a continuous variable and finds
a single value with the highest estimated density. This can be used to
estimate the mode of the data. If there is only one value that value is
returned. If multiple density maxima with the same density exist, their mean
is returned.
}