filteredProfile: An example of a filtered phylogenetic profile

In BIONF/PhyloProfile: PhyloProfile

An example of a filtered phylogenetic profile

Description

An example of a filtered phylogenetic profile

Usage

data(filteredProfile)

Format

Dataframe

Value

A data frame with 168 rows and 20 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

• numberSpec Total number of species in each supertaxon

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

• presSpec Percentage of taxa having orthologs in each supertaxon

• presentTaxa Number of taxa that have ortho in each supertaxon

• totalTaxa Total number of taxa in each supertaxon

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

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

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.