dcGOR (version 1.0.2)

dcRDataLoader: Function to load dcGOR built-in RData

Description

dcRDataLoader is supposed to load RData that are used by package dcGOR.

Usage

dcRDataLoader(RData = c(NA, "SCOP.sf", "SCOP.fa", "onto.GOBP",
"onto.GOMF",
"onto.GOCC", "onto.DO", "onto.HPPA", "onto.HPMI", "onto.HPON",
"onto.MP",
"onto.EC", "onto.KW", "onto.UP", "SCOP.sf2GOBP", "SCOP.sf2GOMF",
"SCOP.sf2GOCC", "SCOP.sf2DO", "SCOP.sf2HPPA", "SCOP.sf2HPMI",
"SCOP.sf2HPON",
"SCOP.sf2MP", "SCOP.sf2EC", "SCOP.sf2KW", "SCOP.sf2UP", "SCOP.fa2GOBP",
"SCOP.fa2GOMF", "SCOP.fa2GOCC", "SCOP.fa2DO", "SCOP.fa2HPPA",
"SCOP.fa2HPMI",
"SCOP.fa2HPON", "SCOP.fa2MP", "SCOP.fa2EC", "SCOP.fa2KW", "SCOP.fa2UP",
"Ancestral_domainome", "eTOL"), domain = c(NA, "SCOP.sf", "SCOP.fa"),
ontology = c(NA, "GOBP", "GOMF", "GOCC", "DO", "HPPA", "HPMI", "HPON",
"MP",
"EC", "KW", "UP"), verbose = T,
RData.location = "http://supfam.org/dcGOR/data")

Arguments

RData

which built-in RData to load. If NOT NA, this RData will be always loaded. It can be: domains (including 'SCOP.sf', 'SCOP.fa'), ontologies (including 'onto.GOBP', 'onto.GOMF', 'onto.GOCC', 'onto.DO', 'onto.HPPA', 'onto.HPMI', 'onto.HPON', 'onto.MP', 'onto

domain

domain part of annotation RData to load. When RData is NA and this plus next are NOT NA, then this plus next one are used to specify which annotation RData to load. In addition to NA, it can also be: 'SCOP.sf', 'SCOP.fa'

ontology

ontology part of annotation RData to load. This only works together with the previous 'domain' parameter. In addition to NA, it can also be: 'GOBP', 'GOMF', 'GOCC', 'DO', 'HPPA', 'HPMI', 'HPON', 'MP', 'EC', 'KW', 'UP'

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to TRUE for display

RData.location

the characters to tell the location of built-in RData files. By default, it remotely locates at "http://supfam.org/dnet/data" or "https://github.com/hfang-bristol/dcGOR/data". For the user equipped with fast internet connection, this option can be just le

Value

• any use-specified variable that is given on the right side of the assigement sign '<-', which contains the loaded RData.

See Also

dcEnrichment

Examples

# Always, load from specified RData directly
SCOP.sf <- dcRDataLoader(RData='SCOP.sf')
onto.GOMF <- dcRDataLoader(RData='onto.GOMF')
# But for annotaion data, there are two ways to do so:
# 1) in a direct way
SCOP.sf2GOMF <- dcRDataLoader(RData='SCOP.sf2GOMF')
# 2) in an indirect way: specify both domain and ontology
SCOP.sf2GOMF <- dcRDataLoader(domain='SCOP.sf', ontology='GOMF')