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adjacency: Make distance estimation customizable

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This commit is contained in:
Elias Projahn 2022-01-09 20:21:27 +01:00
parent ac9894e988
commit 2ceda0691b
4 changed files with 109 additions and 71 deletions
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10
man/adjacency.Rd
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@ -4,13 +4,15 @@
\alias{adjacency}
\title{Score genes based on their proximity to the reference genes.}
\usage{
adjacency()
adjacency(estimate = densest)
}
\arguments{
\item{estimate}{A function that will be used to summarize the distance
values for each gene. See \code{\link[=densest]{densest()}} for the default implementation.}
}
\value{
An object of class \code{geposan_method}.
}
\description{
This method finds the distance value with the maximum density for each gene
(i.e. the mode of its estimated distribution). Genes are scored by comparing
those distance values with the values of the reference genes.
Score genes based on their proximity to the reference genes.
}

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.
}