View source: R/summary_genome.R
summary_genome | R Documentation |
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.
summary_genome(file, organism)
file |
file path to a genome assembly file in |
organism |
character string specifying the organism at hand. |
The summary statistics include:
genome_size_mbp
: Genome size in mega base pairs
n50_mbp
: The N50 contig size of the genome assembly in mega base pairs
n_seqs
: The number of chromosomes/scaffolds/contigs of the genome assembly file
n_nnn
: The absolute number of NNNs (over all chromosomes or scaffolds or contigs) in the genome assembly file
rel_nnn
: The percentage (relative frequency) of NNNs (over all chromosomes or scaffolds or contigs) compared to the total number of
nucleotides in the genome assembly file
genome_entropy
: The Shannon Entropy
of the genome assembly file (median entropy over all individual chromosome entropies)
n_gc
: The total number of GCs
(over all chromosomes or scaffolds or contigs) in the genome assembly file
rel_gc
: The (relative frequency) of GCs
(over all chromosomes or scaffolds or contigs) compared to the total number of
nucleotides in the genome assembly file
Hajk-Georg Drost
summary_cds
, getCollection
, getGenome
, read_genome
## 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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.