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Add species adjacency method

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Elias Projahn 2022-01-17 20:11:07 +01:00
parent c8f1e522f9
commit 53f955f3da
6 changed files with 202 additions and 14 deletions
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16
man/adjacency.Rd
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@ -4,13 +4,14 @@
\alias{adjacency}
\title{Score genes based on their proximity to the reference genes.}
\usage{
adjacency(estimate = densest, combination = min)
adjacency(distance_estimate = densest, summarize = min)
}
\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.}
\item{distance_estimate}{A function that will be used to summarize the
distance 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
\item{summarize}{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
the distance to the nearest reference gene will be scored.}
}
@ -18,5 +19,10 @@ the distance to the nearest reference gene will be scored.}
An object of class \code{geposan_method}.
}
\description{
Score genes based on their proximity to the reference genes.
In this case, the distance data that is available for one gene is first
combined. The resulting value is compared to the reference genes and
determines the gene's score in relation to other genes.
}
\seealso{
\code{\link[=species_adjacency]{species_adjacency()}}
}

25
man/species_adjacency.Rd Normal file
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@ -0,0 +1,25 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/species_adjacency.R
\name{species_adjacency}
\alias{species_adjacency}
\title{Score genes based on their adjacency to the reference genes within species.}
\usage{
species_adjacency(distance_estimate = min, summarize = stats::median)
}
\arguments{
\item{distance_estimate}{Function for combining the distance differences
within one species.}
\item{summarize}{Function for summarizing the distance values across species.}
}
\value{
An object of class \code{geposan_method}.
}
\description{
For each gene and species, the method will first combine the gene's distances
to the reference genes within that species. Afterwards, the results are
summarized across species and determine the gene's score.
}
\seealso{
\code{\link[=adjacency]{adjacency()}}
}