getMatch: Species matching function

In CHuanSite/SJD: Structured Joint Decomposition (SJD)

Species matching function

Description

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).

Examples

data(NeuroGenesis4)
out = getMatch(
rownames(NeuroGenesis4$Meissner.inVitro.bulk.Hs),
inSpecies = 'human',
inType = 'symbol',
newSpecies = 'mouse')

CHuanSite/SJD documentation built on Nov. 29, 2024, 5:52 a.m.