catDB-class {systemPipeR}

R Documentation

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)

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