gpdata_orthodb_v101: Data package used in evolutionary root inference...

In leofields/geneplast.data.orthodb.v101: Input data for the geneplast package

Description

Data package used in evolutionary root inference reconstruction containing four objects derived from the OrthoDB database, release 10.1

Usage

data(gpdata_orthodb_v101)

Format

Dataset with cogids, cogdata, sspids, phyloTree.

• cogids. A data.frame with 406503 COG IDs.

• cogdata. A data.frame with COG to protein mapping.

  • protein_id. Proteins listed in the COG data information.

  • ssp_id. Species listed in the COG data information.

  • cog_id. COG identifiers.

• sspids. A data.frame with species identifiers.

  • ssp_id. Species identifier. Same as NCBI taxonomy identifier.

  • ssp_name. Name of the species.

  • domain. Species domain.

• phyloTree. An object of class 'phylo'.

  • Phylogenetic tree with 1258 tips and 719 internal nodes describing relations between all Eukaryotes listed in the 'sspids' object.

Source

https://www.orthodb.org/

leofields/geneplast.data.orthodb.v101 documentation built on April 14, 2020, 11:37 a.m.