getOMAGroup: Retrieve an OMA Group from the OMA Browser

Description Usage Arguments Details Value Examples

View source: R/getOMAGroup.R

Description

This function obtains an OMA Group from the OMA Browser database. An OMA Group is defined to be a clique of proteins that are all orthologous to each other, i.e. they are all related through speciation events only. An OMA Group can thus by definition not contain any inparalogs. It is a very stringent orthology grouping approach. OMA Groups are mostly useful to infer phylogenetic species tree where they can be used as marker genes.

Usage

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getOMAGroup(id, attribute = NULL)

Arguments

id

An identifier for the group. See above for possible types of IDs.

attribute

an extra attribute to be returned (close_groups)

Details

Retrieving an OMA Group can be done using a group nr as id, its fingerprint (a 7mer AA sequence which is unique to proteins in that group), a member protein id or any sequence pattern that is unique to the group.

Value

an object containing the JSON keys as attributes or a dataframe

Examples

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getOMAGroup(id='58')
getOMAGroup(id='P12345')
getOMAGroup(id='NNRRGRI')
getOMAGroup(id='58', attribute='close_groups')

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