annotation_get: Get GO annotations

In MahShaaban/rkip: Gene co-expression analysis of RKIP, autophagy and EMT in prostate cancer

Description

Get Gene Ontology (GO) annotations is a tidy data.frame. This function is customized to extract the lower level GO IDs before finding the gene products associated with each ID. Finally, the term corresponding to each ID is added

Usage

annotation_get(go_id, go_names, go_db, go_term, org_db, columns,
  remove_predicted = TRUE, ...)

Arguments

go_id	A character vector of GO IDs
go_names	A character vector of GO category names
go_db	A GO.db object
go_term	A GO.db object for GO terms
org_db	An organism object
columns	A charachter vector
remove_predicted	A logical (default, TRUE) for removing predicted genes
...	Other arguments passed to select

Value

A data.frame of at least 6 columns

• category The category/ies as in go_names

• go The GO ID/s as in go_id or their lower level components

• evidence The type of evidence for each gene product

• ontology The type of ontology (e.g. BP, MF and/or CC)

• (column/s) The query columns as in columns

• term The term corresponding to each GO ID

Examples

## Not run: 
# load required libraries
library(org.Mm.eg.db)
library(GO.db)

# prepare query
go_ids <- c('GO:0006914', 'GO:0004679')
go_names <- c('autophagy', 'AMPK')
go_db <- GOBPCHILDREN
go_term <- GOTERM
org_db <- org.Mm.eg.db
columns <- 'SYMBOL'

# call function
ann <- annotation_get(go_ids,
                      go_names,
                      go_db,
                      go_term,
                      org_db,
                      columns)

## End(Not run)

MahShaaban/rkip documentation built on May 23, 2019, 8:37 a.m.