findOrthologs: map orthologous genes using ENSEMBL BioMART

In vitkl/orthologsBioMART: Convenient functions for mapping orthologous genes using ENSEMBL BioMART

Description

findOrthologs(): map orthologous genes using ENSEMBL BioMART (getBM) from one species to another species. This function retrieves ids by 500 at a time to decrease the load on ENSEMBL servers.

findOrthologsHsMm(): map orthologous genes using ENSEMBL BioMART from human to mouse

findOrthologsMmHs(): map orthologous genes using ENSEMBL BioMART from mouse to human

loadBIOMARTdatasets(): Load 2 ENSEMBL BioMART datasets for finding orthologs. Details useMart

attributesFiltersFromTo(): List filters and attributes available in each dataset. Details: listAttributes

Usage

findOrthologs(datasets_FROM_TO = loadBIOMARTdatasets(from =
  "hsapiens_gene_ensembl", to = "mmusculus_gene_ensembl"),
  from_filters = "hgnc_symbol", from_values = c("TP53", "TERT"),
  to_attributes = "external_gene_name",
  to_homolog_attribute = "mmusculus_homolog_ensembl_gene",
  from_gene_id_name = "human_ensembl_gene_id",
  to_gene_id_name = "mouse_ensembl_gene_id")

findOrthologsHsMm(from_filters = "hgnc_symbol", from_values = c("TP53",
  "TERT"), to_attributes = "external_gene_name")

findOrthologsMmHs(from_filters = "ensembl_gene_id",
  from_values = c("ENSMUSG00000059552", "ENSMUSG00000021611"),
  to_attributes = "hgnc_symbol")

loadBIOMARTdatasets(from = "hsapiens_gene_ensembl",
  to = "mmusculus_gene_ensembl")

attributesFiltersFromTo(datasets_FROM_TO = loadBIOMARTdatasets())

Arguments

datasets_FROM_TO	environment containing "Mart" objects produced by loadBIOMARTdatasets(). It is convenient to specify datasets here rather than pre-loading. Full list of datasets in ENSEMBL BioMART: listDatasets("ensembl")
from_filters	Filters (one or more) that should be used in the query in the "from" species database. A possible list of filters can be retrieved using attributesFiltersFromTo(datasets_FROM_TO = loadBIOMARTdatasets()).
from_values	Values of the filter, e.g. vector of affy IDs in the "from" species database. If multiple filters are specified then the argument should be a list of vectors of which the position of each vector corresponds to the position of the filters in the filters argument. Please limit the number of values to less than 500.
to_attributes	Attributes you want to retrieve from the "to" species database. A possible list of attributes can be retrieved using the function attributesFiltersFromTo(datasets_FROM_TO = loadBIOMARTdatasets()).
to_homolog_attribute	Attribute that returns homolog gene id in the "from" database
from_gene_id_name	name of the column containing the ENSEMBL gene ids of "from" species
to_gene_id_name	name of the column containing the ENSEMBL gene ids of "from" species
from	ENSEMBL biomart dataset for a species whose identifiers you want to convert. Full list of possible options: listDatasets("ensembl")
to	ENSEMBL biomart dataset for a species whose identifiers you want convert into.
datasets_FROM_TO	environment containing "Mart" objects produced by loadBIOMARTdatasets()

Value

findOrthologs(): data.frame containing the mapping of homologous genes from one species to another species including to_attributes

findOrthologsHsMm(): data.frame containing the mapping of homologous genes from human to mouse including to_attributes

findOrthologsMmHs(): data.frame containing the mapping of homologous genes from mouse to human including to_attributes

loadBIOMARTdatasets(): environment containing 2 object of class 'Mart', one for each species dataset

attributesFiltersFromTo(): list containing 4 vector of either filters or attributes for each dataset

Author(s)

Vitalii Kleshchevnikov

Examples

findOrthologs()
findOrthologsHsMm()
findOrthologsMmHs()
attributes = attributesFiltersFromTo(datasets_FROM_TO = loadBIOMARTdatasets())
grep("Mouse gene stable ID", attributes$from_attributes$description, ignore.case = T, value = T)
attributes$from_attributes[which(attributes$from_attributes$description == "Mouse gene name"),]
grep("hgnc_symbol", attributes$from_attributes$name, value = T)
# find the desired column name
attributes$from_attributes[grep("Mouse gene stable ID", attributes$from_attributes$description, ignore.case = T),]

vitkl/orthologsBioMART documentation built on Nov. 15, 2021, 9:20 p.m.