Use biomaRt to retrieve additional gene identifiers for a vector of gene identifiers in one species (e.g. 'human'), or gene identifiers for orthologous genes in a second species (e.g. 'mouse')
Usage
getMatch(
genes,
inSpecies,
inType,
newSpecies,
useNewestVersion = FALSE,
moreAttrIn = NA,
moreAttrNew = NA
)Arguments
- genes
character vector of gene identifiers in either ensembl gene identifier or gene symbol format
- inSpecies
a character vector indicating the species from which 'genes' come; must be one of: "human", "mouse", "roundworm", "fruitfly", "zebrafish", "chicken", "rat", "guinea pig", "golden hamster", "rabbit","pig", "sheep", "cow", "dog", "cat", "macaque", "bonobo", "chimpanzee"
- inType
a single character value indicating the type of gene identifiers being passed in the "genes" argument; must be one of: "symbol", "ensembl"
- newSpecies
a character vector indicating the species for which orthologous gene identifiers are desired; must be one of: "human", "mouse", "roundworm", "fruitfly", "zebrafish", "chicken", "rat", "guinea pig", "golden hamster", "rabbit", "pig", "sheep", "cow", "dog", "cat", "macaque", "bonobo", "chimpanzee"
- useNewestVersion
logical indicating if the function should attempt to use the latest version of ensembl, or to use the Aug 2020 archive version that is more stable. default is FALSE.
- moreAttrIn
character vector of other gene attributes that you want returned for the input species from biomaRt - to add this argument you must know the names of the fields in the species-specific biomaRt that you are requesting. default is NA.
- moreAttrNew
character vector of other gene attributes that you want returned for the output species from biomaRt - to add this argument you must know the names of the fields in the species-specific biomaRt that you are requesting. default is NA.
Value
A matrix whose first column contains the exact gene identifiers (and in the same order) that were sent to the function in the "genes" argument, followed by 3 columns of gene identifiers that were retrieved from biomaRt from both the "inSpecies" and the "newSpecies" (for each species, these 3 identifiers are: gene symbol, ensembl gene ID, and text description).