getHOG: Retrieve a HOG from the OMA Browser

Description Usage Arguments Details Value Examples

View source: R/getHOG.R

Description

The function retrieves a specific Hierarchical Orthologous Group (HOG) from the OMA Browser database. A HOG is a set of genes that have all decendet from a single ancestral gene at a specific taxonomic level.

Usage

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getHOG(id, level = NULL, members = FALSE)

Arguments

id

an identifier for the HOG to be returned - either its HOG ID or a protein id.

level

a specific level for the HOG to be restricted to. level can either be 'root', or the name of a taxonomic level that is part of the HOG, e.g. 'Fungi'. By default it will retrieve the depest level of the most specific subhog for the given ID.

members

boolean that when set to TRUE returns a dataframe containg the protein members at a given hog level

Details

A HOG can be identified by its member proteins and a taxonomic level, or a HOG ID. As a taxonomic level, you can use either 'root' to retrieve the HOG at its deepest level, or the name of NCBI taxonomy level, or leave it out in which case the deepest level that doesn't include a duplication node is used.

The function either returns a single hog object or a list of hog objects. The later happens if the HOG ID you provide has already split into several sub-hogs at the level you indicate.

Value

an object containing HOG attributes, or a list of those

Examples

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getHOG(id = 'YEAST590')
getHOG(id = 'YEAST590', level='root')
getHOG(id = 'YEAST590', level='Saccharomycetaceae', members=TRUE)

klarakaleb/roma documentation built on Nov. 11, 2020, 5:36 a.m.