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

preset: Turn into S3 class

Browse source
This commit is contained in:
Elias Projahn 2021-11-03 14:17:39 +01:00
parent 6494ae8200
commit 55958e0d85
8 changed files with 106 additions and 43 deletions
Download patch file Download diff file Expand all files Collapse all files

2
man/analyze.Rd
View file

@ -7,7 +7,7 @@
analyze(preset, progress = NULL)
}
\arguments{
\item{preset}{The preset to use which can be created using \code{\link[=preset]{preset()}}.}
\item{preset}{The preset to use which should be created using \code{\link[=preset]{preset()}}.}
\item{progress}{A function to be called for progress information. The
function should accept a number between 0.0 and 1.0 for the current

3
man/distances.Rd
View file

@ -5,10 +5,11 @@
\alias{distances}
\title{Information on gene positions across species.}
\format{
A \link{data.table} with 1390730 rows and 3 variables:
A \link{data.table} with 1506182 rows and 4 variables:
\describe{
\item{species}{Species ID}
\item{gene}{Gene ID}
\item{position}{Gene start position}
\item{distance}{Distance to nearest telomere}
}
}

17
man/preset.Rd
View file

@ -1,19 +1,24 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/analyze.R
% Please edit documentation in R/preset.R
\name{preset}
\alias{preset}
\title{Create a new preset.}
\usage{
preset(methods, species, genes, reference_genes)
preset(
methods = c("clusteriness", "correlation", "neural", "proximity"),
species_ids = NULL,
gene_ids = NULL,
reference_gene_ids = NULL
)
}
\arguments{
\item{methods}{IDs of methods to apply.}
\item{methods}{Methods to apply.}
\item{species}{IDs of species to include.}
\item{species_ids}{IDs of species to include.}
\item{genes}{IDs of genes to screen.}
\item{gene_ids}{IDs of genes to screen.}
\item{reference_genes}{IDs of reference genes to compare to.}
\item{reference_gene_ids}{IDs of reference genes to compare to.}
}
\value{
The preset to use with \code{\link[=analyze]{analyze()}}.

14
man/print.geposan_preset.Rd Normal file
View file

@ -0,0 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preset.R
\name{print.geposan_preset}
\alias{print.geposan_preset}
\title{S3 method to print a preset object.}
\usage{
\method{print}{geposan_preset}(preset, ...)
}
\description{
S3 method to print a preset object.
}
\seealso{
\code{\link[=preset]{preset()}}
}

2
man/species.Rd
View file

@ -5,7 +5,7 @@
\alias{species}
\title{Information on included species from the Ensembl database.}
\format{
A \link{data.table} with 91 rows and 2 variables:
A \link{data.table} with 99 rows and 2 variables:
\describe{
\item{id}{Unique species ID}
\item{name}{Human readable species name}