get_genome_stats: Get summary statistics for genomes on NCBI using the NCBI...
In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses
View source: R/genome_assembly.R
get_genome_stats R Documentation
Get summary statistics for genomes on NCBI using the NCBI Datasets API
Description
Get summary statistics for genomes on NCBI using the NCBI Datasets API
Usage
get_genome_stats(taxon = NULL, filters = NULL)
Arguments
taxon
Taxon for which summary statistics will be
retrieved, either as a character scalar (e.g., "brassicaceae") or
as a numeric scalar representing NCBI Taxonomy ID (e.g., 3700).
filters
(optional) A list of filters to use when querying the API
in the form of key-value pairs, with keys in list names and values in list
elements (e.g., list(filters.reference_only = "true"), see
examples for details).
Details
Possible filters for the filters parameter can be accessed
at https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/#get-/genome/taxon/-taxons-/dataset_report.
Value
A data frame with the following variables:
- accession
character, accession number.
- source
character, data source.
- species_taxid
numeric, NCBI Taxonomy ID.
- species_name
character, species' scientific name.
- species_common_name
character, species' common name.
- species_ecotype
character, species' ecotype.
- species_strain
character, species' strain.
- species_isolate
character, species' isolate.
- species_cultivar
character, species' cultivar.
- assembly_level
factor, assembly level ("Complete", "Chromosome", "Scaffold", or "Contig").
- assembly_status
character, assembly status.
- assembly_name
character, assembly name.
- assembly_type
character, assembly type.
- submission_date
character, submission date (YYYY-MM-DD).
- submitter
character, submitter name.
- sequencing_technology
character, sequencing technology.
- atypical
logical, indicator of wheter the genome is atypical.
- refseq_category
character, RefSeq category.
- chromosome_count
numeric, number of chromosomes.
- sequence_length
numeric, total sequence length.
- ungapped_length
numeric, ungapped sequence length.
- contig_count
numeric, number of contigs.
- contig_N50
numeric, contig N50.
- contig_L50
numeric, contig L50.
- scaffold_N50
numeric, contig N50.
- scaffold_L50
numeric, contig L50.
- GC_percent
numeric, GC percentage (0-100).
- annotation_provider
character, name of annotation provider.
- annotation_release_date
character, annotation release date (YYYY-MM-DD).
- gene_count_total
numeric, total number of genes.
- gene_count_coding
numeric, number of protein-coding genes.
- gene_count_noncoding
numeric, number of non-coding genes.
- gene_count_pseudogene
numeric, number of pseudogenes.
- gene_count_other
numeric, number of other genes.
- CC_ratio
numeric, ratio of the number of contigs to the number of chromosomes.
Examples
# Example 1: Search for A. thaliana genomes by tax ID
ex1 <- get_genome_stats(taxon = 3702)
# Example 2: Search for A. thaliana genomes by name
ex2 <- get_genome_stats(taxon = "Arabidopsis thaliana")
# Example 3: Search for chromosome-level Brassicaeae genomes
ex3 <- get_genome_stats(
taxon = "brassicaceae",
filters = list(filters.assembly_level = "chromosome")
)
almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.
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View source: R/genome_assembly.R
| get_genome_stats | R Documentation |
Get summary statistics for genomes on NCBI using the NCBI Datasets API
Description
Get summary statistics for genomes on NCBI using the NCBI Datasets API
Usage
get_genome_stats(taxon = NULL, filters = NULL)
Arguments
taxon |
Taxon for which summary statistics will be retrieved, either as a character scalar (e.g., "brassicaceae") or as a numeric scalar representing NCBI Taxonomy ID (e.g., 3700). |
filters |
(optional) A list of filters to use when querying the API
in the form of key-value pairs, with keys in list names and values in list
elements (e.g., |
Details
Possible filters for the filters parameter can be accessed at https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/#get-/genome/taxon/-taxons-/dataset_report.
Value
A data frame with the following variables:
- accession
character, accession number.
- source
character, data source.
- species_taxid
numeric, NCBI Taxonomy ID.
- species_name
character, species' scientific name.
- species_common_name
character, species' common name.
- species_ecotype
character, species' ecotype.
- species_strain
character, species' strain.
- species_isolate
character, species' isolate.
- species_cultivar
character, species' cultivar.
- assembly_level
factor, assembly level ("Complete", "Chromosome", "Scaffold", or "Contig").
- assembly_status
character, assembly status.
- assembly_name
character, assembly name.
- assembly_type
character, assembly type.
- submission_date
character, submission date (YYYY-MM-DD).
- submitter
character, submitter name.
- sequencing_technology
character, sequencing technology.
- atypical
logical, indicator of wheter the genome is atypical.
- refseq_category
character, RefSeq category.
- chromosome_count
numeric, number of chromosomes.
- sequence_length
numeric, total sequence length.
- ungapped_length
numeric, ungapped sequence length.
- contig_count
numeric, number of contigs.
- contig_N50
numeric, contig N50.
- contig_L50
numeric, contig L50.
- scaffold_N50
numeric, contig N50.
- scaffold_L50
numeric, contig L50.
- GC_percent
numeric, GC percentage (0-100).
- annotation_provider
character, name of annotation provider.
- annotation_release_date
character, annotation release date (YYYY-MM-DD).
- gene_count_total
numeric, total number of genes.
- gene_count_coding
numeric, number of protein-coding genes.
- gene_count_noncoding
numeric, number of non-coding genes.
- gene_count_pseudogene
numeric, number of pseudogenes.
- gene_count_other
numeric, number of other genes.
- CC_ratio
numeric, ratio of the number of contigs to the number of chromosomes.
Examples
# Example 1: Search for A. thaliana genomes by tax ID
ex1 <- get_genome_stats(taxon = 3702)
# Example 2: Search for A. thaliana genomes by name
ex2 <- get_genome_stats(taxon = "Arabidopsis thaliana")
# Example 3: Search for chromosome-level Brassicaeae genomes
ex3 <- get_genome_stats(
taxon = "brassicaceae",
filters = list(filters.assembly_level = "chromosome")
)
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