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

Description Usage Arguments Details Value

View source: R/homologue_functions.R

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

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

`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'.
`one_to_one`	Boolean. Should the function only return one-to-one homology mappings?

Note: This function is used in project 'dtg_rnaseq'. But the version there uses dot-separated argument names. The argnames have been converted to underscore-separated. If this function-script is copied back into the 'dtg_rnaseq' project you will have to double-check the function-calls.

A 'data.frame' with columns 'id_sp1' and 'id_sp2'.

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