load_orgdb_annotations: Load organism annotation data from an orgdb sqlite package.

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

Load organism annotation data from an orgdb sqlite package.

Description

Creates a dataframe gene and transcript information for a given set of gene ids using the AnnotationDbi interface.

Usage

load_orgdb_annotations(
  orgdb = NULL,
  gene_ids = NULL,
  include_go = FALSE,
  keytype = "gid",
  location_column = "annot_location_text",
  type_column = "annot_gene_type",
  name_column = "annot_gene_product",
  fields = NULL,
  sum_exon_widths = FALSE
)

Arguments

orgdb	OrganismDb instance.
gene_ids	Search for a specific set of genes?
include_go	Ask the Dbi for gene ontology information?
keytype	Primary key of the tables, 'gid' for EuPathDB data.
location_column	Which column contains the location data for the genes?
type_column	Use this column to identify the gene type.
name_column	Use this column to identify the gene name.
fields	Columns included in the output.
sum_exon_widths	Perform a sum of the exons in the data set?

Details

This defaults to a few fields which I have found most useful, but the brave or pathological can pass it 'all'.

Value

Table of geneids, chromosomes, descriptions, strands, types, and lengths.

Author(s)

atb

See Also

AnnotationDbi GenomicFeatures BiocGenerics columns keytypes select exonsBy

Examples

## Not run: 
 one_gene <- load_orgdb_annotations(org, c("LmJF.01.0010"))

## End(Not run)

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.