get_annotations: Get annotations from databases

In wulingyun/CopTea: Combinatorial OPTimization based Enrichment Analysis

Description

Get the annotations needed for functional enrichment analysis from the databases, including GO and KEGG/Reactome pathway annotations, gene to protein mapping, protein interaction network.

Usage

get_annotations(
  species,
  filters = c("GO", "KEGG", "Reactome", "OMIM"),
  STRING.version = "10",
  STRING.threshold = 900
)

Arguments

species	A string indicated species name, currently support "Human", "Mouse" and "Yeast".
filters	A vector of string indicated the annotations used, currently support "GO", "KEGG", "Reactome", and "OMIM" (only valid for Human).
STRING.version	A string indicated the version number of STRING database used for extracting protein interaction network.
STRING.threshold	A integer number (0-1000) indicated the threshold for extracting network from STRING database.

Value

This function will return a list with the following components:

anno.matrix	A logical matrix indicated the annotations, with each row represents a gene and each column denotes a term. The row names and column names are set as the corresponding gene and term ID respectively.
network	A logical matrix indicated the association (interaction) between genes, which is aggregated from the protein association (interaction) network provided by the STRING database.
gene2protein	A logical matrix indicated the mapping from gene to protein, with each row represents a gene and each column denotes a protein. The row names and column names are set as the corresponding gene and protein ID respectively.
genes	A vector of gene IDs.
terms	A vector of term IDs.
proteins	A vector of protein IDs.
term.info	A matrix of term information, with three columns: Term ID, Term category, and Term description. The row names are set as Term ID.

wulingyun/CopTea documentation built on Dec. 4, 2019, 2:59 p.m.