arabidopsis: Arabidopsis thaliana vignette data

In arendsee/phylostratr: Analyze phylostratigraphic data

Arabidopsis thaliana vignette data

Description

A data frame with the following columns:

Usage

arabidopsis

Format

data.frame

Details

1. qseqid unique gene identifier for the focal species query

2. staxid subject NCBI taxon ID

3. evalue BLAST e-value for the best hit of qseqid against staxid

4. score raw score for the best hit

5. mrca Most Recent Common Ancestor of the query and subject species

6. ps phylostratum level (where 1 is root)

The Arabidopsis thaliana gene models are from the Araport11 annotation. Only 1/100 of the proteins are used (sampled via the regular expression 'AT.G.99' on the TAIR model IDs). The TAIR model ids have the format 'AT<chromosome number>G<position>.<model_id>', for example, AT3G30270.2 is the second gene model for the locus AT3G30270 and is located on the 3rd chromosome.

arendsee/phylostratr documentation built on Dec. 31, 2022, 10:22 a.m.