johrpan/geposan
1
0
Fork 0
mirror of https://github.com/johrpan/geposan.git synced 2025-10-26 10:47:25 +01:00
Code Issues Projects Releases Packages Wiki Activity Actions

Small documentation improvements

Browse source
This commit is contained in:
Elias Projahn 2023-09-27 13:24:23 +02:00
parent 3e19f53d2a
commit 44e170f5a6
4 changed files with 8 additions and 2 deletions
Download patch file Download diff file Expand all files Collapse all files

2
R/method_clustering.R
View file

@ -56,6 +56,8 @@ clusteriness <- function(data, span = 500000, weight = 0.5) {
#' @param id Unique ID for the method and its results. #' @param id Unique ID for the method and its results.
#' @param name Human readable name for the method. #' @param name Human readable name for the method.
#' @param description Method description. #' @param description Method description.
#' @param span See [clusteriness()].
#' @param weight See [clusteriness()].
#' #'
#' @return An object of class `geposan_method`. #' @return An object of class `geposan_method`.
#' #'

2
R/preset.R
View file

@ -6,7 +6,7 @@
#' filtered based on how many species have data for them. Afterwards, species #' filtered based on how many species have data for them. Afterwards, species
#' that still have many missing genes will also be excluded. See the different #' that still have many missing genes will also be excluded. See the different
#' method functions for the available methods: [clustering()], [correlation()], #' method functions for the available methods: [clustering()], [correlation()],
#' [neural()], [adjacency()] and [species_adjacency()]. #' [distance()], [neural()] and [random_forest()].
#' #'
#' @param reference_gene_ids IDs of reference genes to compare to. #' @param reference_gene_ids IDs of reference genes to compare to.
#' @param methods List of methods to apply. #' @param methods List of methods to apply.

4
man/clustering.Rd
View file

@ -18,6 +18,10 @@ clustering(
\item{name}{Human readable name for the method.} \item{name}{Human readable name for the method.}
\item{description}{Method description.} \item{description}{Method description.}
\item{span}{See \code{\link[=clusteriness]{clusteriness()}}.}
\item{weight}{See \code{\link[=clusteriness]{clusteriness()}}.}
} }
\value{ \value{
An object of class \code{geposan_method}. An object of class \code{geposan_method}.

2
man/preset.Rd
View file

@ -38,5 +38,5 @@ reference genes to be able to assess the results later. The genes will be
filtered based on how many species have data for them. Afterwards, species filtered based on how many species have data for them. Afterwards, species
that still have many missing genes will also be excluded. See the different that still have many missing genes will also be excluded. See the different
method functions for the available methods: \code{\link[=clustering]{clustering()}}, \code{\link[=correlation]{correlation()}}, method functions for the available methods: \code{\link[=clustering]{clustering()}}, \code{\link[=correlation]{correlation()}},
\code{\link[=neural]{neural()}}, \code{\link[=adjacency]{adjacency()}} and \code{\link[=species_adjacency]{species_adjacency()}}. \code{\link[=distance]{distance()}}, \code{\link[=neural]{neural()}} and \code{\link[=random_forest]{random_forest()}}.
} }