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42 lines
1.5 KiB
R
42 lines
1.5 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/preset.R
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\name{preset}
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\alias{preset}
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\title{Create a new preset.}
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\usage{
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preset(
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reference_gene_ids,
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methods = all_methods(),
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species_ids = geposan::species$id,
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gene_ids = geposan::genes$id,
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species_requirement = 0.25,
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gene_requirement = 0.5
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)
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}
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\arguments{
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\item{reference_gene_ids}{IDs of reference genes to compare to.}
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\item{methods}{List of methods to apply.}
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\item{species_ids}{IDs of species to include.}
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\item{gene_ids}{IDs of genes to screen.}
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\item{species_requirement}{The proportion of species a gene has to have
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orthologs in in order for the gene to qualify.}
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\item{gene_requirement}{The proportion of genes that a species has to have
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in order for the species to be included in the analysis.}
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}
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\value{
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The preset to use with \code{\link[=analyze]{analyze()}}.
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}
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\description{
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A preset is used to specify which methods and inputs should be used for an
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analysis. Note that the genes to process should normally include the
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reference genes to be able to assess the results later. The genes will be
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filtered based on how many species have data for them. Afterwards, species
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that still have many missing genes will also be excluded. See the different
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method functions for the available methods: \code{\link[=clustering]{clustering()}}, \code{\link[=correlation]{correlation()}},
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\code{\link[=distance]{distance()}}, \code{\link[=neural]{neural()}} and \code{\link[=random_forest]{random_forest()}}.
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}
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