getGeneIds: Get Gene.id values for a list of gene identifiers

In InterMineR: R Interface with InterMine-Powered Databases

Description

This function takes as input a list of gene identifiers and retrieves their unique Gene.id values for a specific organism.

Usage

getGeneIds(im, genes, organism)

Arguments

im	a list containing the base URL and API token.
genes	a character vector containing the gene identifiers.
organism	a character string for the name of the Organism.

Details

This function is designed to work in conjuction with the doEnrichment function.

Value

getGeneIds returns a list containing a data.frame of unique gene identifiers as well as the Gene.id values as a comma-separated string, ready to be used as input for the ids argument of the doEnrichment function.

Furthermore, in case of genes that return multiple identifiers or no identifiers, these are also reported separately in a data.frame and a character vector respectively.

unique.results	data.frame with unique gene identifiers
doEnrichment.string	comma-separated character string of Gene.id values
multiple.results	data.frame with genes returning multiple identifiers
genes.with.no.results	character vector with genes returning no identifiers

Note

doEnrichment.string can be passed as input in the doEnrichment function.

Author(s)

InterMine Team

See Also

getWidgets, doEnrichment

Examples

# HumanMine and Homo sapiens genes 
hsa.genes <- c("ABCC8", "ACE", "AKT2", "APPL1", "AQP2", "AVP", "AVPR2", "BLK", "CAPN10", "CCR5")

list.hsa <- getGeneIds(
  im = initInterMine(listMines()["HumanMine"]),
  organism = "Homo sapiens",
  genes = hsa.genes # must be a character vector!!!
)

# FlyMine and Drosophila melanogaster genes
fly.genes <- c("fkh", "vvl", "BEAF-32", "Antp", "Scr", "abd-A", "bcd", "Ubx", "zen", "ara")

list.fly <- getGeneIds(
  im = initInterMine(listMines()["FlyMine"]),
  organism = "Drosophila melanogaster",
  genes = fly.genes # must be a character vector!!!
)

InterMineR documentation built on Nov. 8, 2020, 5:58 p.m.