filteredProfile {PhyloProfile} | R Documentation

## An example of a filtered phylogenetic profile.

### Description

An example of a filtered phylogenetic profile.

### Usage

    data(filteredProfile)

### Format

A data frame with 168 rows and 18 variables:

- geneID Seed or ortholog group ID, e.g. "100136at6656"

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

- ncbiID Taxon ID, e.g. "ncbi10116"

- orthoID Ortholog ID, e.g. "100136at6656|HUMAN@9606@1|Q9UNQ2|1"

- 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. "ncbi9606"

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

- fullName Full taxon name of the ortholog, e.g. "Homo sapiens"

- 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

- 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

- taxonMod Name of supersupertaxon w/o its index, e.g. "Mammalia"

- presSpec Percentage of taxa that have ortho in each supertaxon

[Package PhyloProfile version 1.4.11 Index]