preset: Create a new preset.
In johrpan/geposan: Gene Position Analysis

preset

R Documentation

Create a new preset.

Description

A preset is used to specify which methods and inputs should be used for an analysis. Note that the genes to process should normally include the 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 that still have many missing genes will also be excluded. See the different method functions for the available methods: distance(), variation(), clustering(), adjacency(), correlation() and random_forest().

Usage

preset(
  reference_gene_ids,
  methods = all_methods(),
  species_ids = geposan::species$id,
  gene_ids = geposan::genes$id,
  species_requirement = 0.25,
  gene_requirement = 0.5
)

Arguments

`reference_gene_ids`	IDs of reference genes to compare to.
`methods`	List of methods to apply.
`species_ids`	IDs of species to include.
`gene_ids`	IDs of genes to screen.
`species_requirement`	The proportion of species a gene has to have orthologs in in order for the gene to qualify.
`gene_requirement`	The proportion of genes that a species has to have in order for the species to be included in the analysis.