catDB-class: Class '"catDB"'

In tgirke/systemPipeR: systemPipeR: NGS workflow and report generation environment

Class "catDB"

Description

Container for storing mappings of genes to annotation categories such as gene ontologies (GO), pathways or conserved sequence domains. The catmap slot stores a list of data.frames providing the direct assignments of genes to annotation categories (e.g. gene-to-GO mappings); catlist is a list of lists of all direct and indirect associations to the annotation categories (e.g. genes mapped to a pathway); and idconv allows to store a lookup-table for converting identifiers (e.g. array feature ids to gene ids).

Objects from the Class

Objects can be created by calls of the form new("catDB", ...).

Slots

catmap:

Object of class "list" list of data.frames

catlist:

Object of class "list" list of lists

idconv:

Object of class "ANY" list of data.frames

Methods

catlist

signature(x = "catDB"): extracts data from catlist slot

catmap

signature(x = "catDB"): extracts data from catmap slot

coerce

signature(from = "list", to = "catDB"): as(list, "catDB")

idconv

signature(x = "catDB"): extracts data from idconv slot

names

signature(x = "catDB"): extracts slot names

show

signature(object = "catDB"): summary view of catDB objects

Author(s)

Thomas Girke

See Also

makeCATdb, GOHyperGAll, GOHyperGAll_Subset, GOHyperGAll_Simplify, GOCluster_Report, goBarplot

Examples

showClass("catDB")
## Not run: 
## Obtain annotations from BioMart
library("biomaRt")
listMarts()  # To choose BioMart database
listMarts(host = "plants.ensembl.org")
m <- useMart("plants_mart", host = "plants.ensembl.org")
listDatasets(m)
m <- useMart("plants_mart", dataset = "athaliana_eg_gene", host = "plants.ensembl.org")
listAttributes(m)  # Choose data types you want to download
go <- getBM(attributes = c("go_id", "tair_locus", "namespace_1003"), mart = m)
go <- go[go[, 3] != "", ]
go[, 3] <- as.character(go[, 3])
go[go[, 3] == "molecular_function", 3] <- "F"
go[go[, 3] == "biological_process", 3] <- "P"
go[go[, 3] == "cellular_component", 3] <- "C"
go[1:4, ]

dir.create("./data/GO", recursive = TRUE)
write.table(go, "data/GO/GOannotationsBiomart_mod.txt", quote = FALSE, row.names = FALSE,
            col.names = FALSE, sep = "\t")
            
## Create catDB instance (takes a while but needs to be done only once)
catdb <- makeCATdb(myfile = "data/GO/GOannotationsBiomart_mod.txt", lib = NULL, org = "",
                   colno = c(1, 2, 3), idconv = NULL)
catdb
save(catdb, file = "data/GO/catdb.RData")
load("data/GO/catdb.RData")

## End(Not run)

tgirke/systemPipeR documentation built on Aug. 30, 2022, 10 p.m.