ensemblToGo: get requested ensembl ID to GO mapping table

In scGOclust: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq

get requested ensembl ID to GO mapping table

Description

get requested ensembl ID to GO mapping table

Usage

ensemblToGo(
  species,
  GO_type = "biological_process",
  GO_linkage_type = c("standard"),
  ...
)

Arguments

species	species name matching ensembl biomaRt naming, such as hsapiens, mmusculus
GO_type	GO term type, choose among 'biological_process', 'molecular_function', 'cellular_component', default 'biological_process'
GO_linkage_type	GO annotation evidence codes to include. Default is 'standard', which means only including manually checked records (excluding IEA) and excluding those inferred from gene expression experiments to maximally suffice the species expression independence assumption. 'Stringent' means only including those with experimental evidence, also not from gene expression experiment, or from manual curation with evidence (excluding those from mass-annotation pipelines). Choose among 'experimental', 'phylogenetic', 'computational', 'author', 'curator', 'electronic', 'standard', stringent'
...	additional params for useEnsembl function called in this function

Value

a table with ensembl to GO terms mapping including requested linkage type

Examples

library(scGOclust)
library(httr)
httr::set_config(httr::config(ssl_verifypeer = FALSE))
ensemblToGo("mmusculus", GO_type = "biological_process", GO_linkage_type = 'stringent')

scGOclust documentation built on May 29, 2024, 8:59 a.m.