Tool.FindGenesFromGO: Find Genes Annotated in Specific GO Terms

In ZJUDBlab/InterCellDB: Tool and Database for Analyzing Interactions

Find Genes Annotated in Specific GO Terms

Description

This function uses GO terms or GO IDs to get a specific list of genes.

Usage

Tool.FindGenesFromGO(
  go.todolist,
  genes.ref.db,
  go.ref.db,
  go.use.relative = TRUE,
  go.relative.option = "offspring"
)

Arguments

go.todolist	Character. Several GO_terms or GO_IDs or mixed, which will be used to get subsets of feature genes.
genes.ref.db	List. It is taxonomy specific, which contains 3 parts: 1. gene.ncbi.db NCBI-gene database for specific species 2. gene.synonyms.db GeneID-GeneName-Synonym pairs extracted from (1) 3. gene.dup.synonyms.db Some genes may have same synonyms, and this can cause mistakes when match target synonym back to its authorized genename.
go.ref.db	Data.frame. Reference GO database provided in this package, the list is given as follows: For human: go.human.ref.db For mouse: go.mouse.ref.db
go.use.relative	Character. If set TRUE, GO IDs or Terms will be explored by its relatives of GO term tree. This is useful as the lite version of GO database will only records the gene and its most accurate GO terms.
go.relative.option	Character. 4 options: ancestor, parents, offspring, children. With each corresponding to one group of database listed in GO.db.

Value

Character. A gene list of given GO IDs or terms.

ZJUDBlab/InterCellDB documentation built on March 19, 2023, 4:56 p.m.