map_to_homologues_oneway: map_to_homologues_oneway

In russHyde/homologiser: Map Genes To Their Homologues In A Different Species

Description

Takes gene ids from one species and maps them to gene ids in another species. Can convert entrez ids and ensembl ids

Usage

map_to_homologues_oneway(gene_ids = character(0), dataset_sp1 = NULL,
  dataset_sp2 = NULL, sp1 = "hsapiens", sp2 = "mmusculus",
  idtype_sp1 = "ensembl_gene_id", idtype_sp2 = "ensembl_gene_id")

Arguments

gene_ids	A vector of gene identifiers for species 'sp1' and of type 'idtype_sp1'.
dataset_sp1	The 'biomaRt' dataset that houses the data for species 'sp1'.
dataset_sp2	The 'biomaRt' dataset that houses the data for species 'sp2'.
sp1	The name of species 1 (using ensembl prefixes like 'hsapiens' / 'mmusculus').
sp2	The name of species 2 (using ensembl prefixes like 'hsapiens' / 'mmusculus').
idtype_sp1	The type of identifier used for species 'sp1'; this should match one of the field / column names in the biomaRt dataset for species 'sp1'.
idtype_sp2	The type of identifier used for species 'sp2'; this should match one of the field / column names in the biomaRt dataset for species 'sp2'.

Details

— Non-exported function — — All inputs should have been validity-checked by map_to_homologues —

Selects all genes from the biomart dataset for species1 that have homologues in species 2 1) Map input-ids in species 1 to ensembl gene in species 2 2) Map ensembl gene in species 2 to output-ids in species 2

Map species 1 gene_ids to ensembl-ids in species 2 - Since dataset_sp1 is the mart for species 1, we don't have to pass the sp1, host or mart.name arguments into map_to_ensembl_homologues...

russHyde/homologiser documentation built on May 19, 2020, 8:20 p.m.