full_processed_profile: An example of a fully processed phylogenetic profile.

In trvinh/test: PhyloProfile

Description

An example of a fully processed phylogenetic profile.

Usage

full_processed_profile

Format

A data frame with 20 rows and 17 variables:

• supertaxon Supertaxon name together with its ordered index, e.g. "1001_Mammalia"

• geneID Seed or ortholog group ID, e.g. "OG_1017"

• ncbiID Taxon ID, e.g. "ncbi10090"

• orthoID Ortholog ID, e.g. "M.musculus@10090@112934"

• var1 First additional variable

• var2 Second additional variable

• paralog Number of co-orthologs in the current taxon

• abbrName NCBI ID of the ortholog, e.g. "ncbi10090"

• taxonID Taxon ID of the ortholog, in this case: "0"

• fullName Full taxon name of the ortholog, e.g. "Mus musculus"

• supertaxonID Supertaxon ID (only different than ncbiID in case working with higher taxonomy rank than input's). e.g. "40674"

• rank Rank of the supertaxon, e.g. "class"

• category "cat

• presSpec The percentage of species presenting in each supertaxon

• mVar1 Value of the 1. variable after grouping into supertaxon

• mVar2 Value of the 2. variable after grouping into supertaxon

• numberSpec Total number of species in each supertaxon

trvinh/test documentation built on May 9, 2019, 2:26 a.m.