summary_genome {biomartr}R Documentation

Retrieve summary statistics for a genome assembly file

Description

A summary statistics of specific genome features is generated. These statistics are useful to assess the genome quality of retrieved genome assemblies when performing comparative genomics tasks. This way, users can assess whether or not patterns found based on genome comparisons aren't just a technical artifact of differences in genome assembly quality.

Usage

summary_genome(file, organism)

Arguments

file

file path to a genome assembly file in fasta format.

organism

character string specifying the organism at hand.

Details

The summary statistics include:

Author(s)

Hajk-Georg Drost

See Also

summary_cds, getCollection, getGenome, read_genome

Examples

## Not run: 
# retrieve genome from NCBI RefSeq
Sc <- biomartr::getGenome(db = "refseq", organism = "Saccharomyces cerevisiae")
# compute genome assembly summary statistics
Sc_genome_summary <- summary_genome(file = Sc, organism = "Saccharomyces cerevisiae")
# look at results
Sc_genome_summary

## End(Not run)

[Package biomartr version 1.0.7 Index]