loadGeneSummary: Load gene summary table

In jokergoo/GeneSummary: RefSeq Gene Summaries

Load gene summary table

Description

Load gene summary table

Usage

loadGeneSummary(organism = 9606,
    status = c("reviewed", "predicted", "inferred", "validated", "provisional"))

Arguments

organism	Name of the organism (e.g. "Homo sapiens") or the corresponding taxon ID (e.g. 9606).
status	Status of the review of the genes.

Details

The gene summaries are extracted from RefSeq database (https://ftp.ncbi.nih.gov/refseq/release/complete/*.rna.gbff.gz). Gene summaries are available in the "COMMENT" section of the *rna.gbff.gz files.

The Perl script used to parse *rna.gbff.gz files is available in system.file("extdata", "parse_refseq.pl", package = "GeneSummary").

Value

A data frame with the following columns:

RefSeq_accession

RefSeq accession. Note there is also the version number after the accession.

Organism

Full organism name.

Taxon_ID

Taxon ID of the organism.

Gene_ID

Entrez gene ID.

Review_status

Status of the review of the gene.

Gene_summary

A long description of the gene.

Examples

df = loadGeneSummary(9606)
dim(df)
head(df)

jokergoo/GeneSummary documentation built on Sept. 29, 2023, 1:01 p.m.