OlsSearch-class: Class '"OlsSearch"'

In rols: An R interface to the Ontology Lookup Service

Description

Searching the OLS is done using the OlsSearch data structure.

Objects from the Class

Objects can be created with the constructor function OlsSearch.

Slots

q:

Object of class "character" ~~

ontology:

Object of class "character" ~~

type:

Object of class "character" ~~

slim:

Object of class "character" ~~

fieldList:

Object of class "character" ~~

queryFields:

Object of class "character" ~~

exact:

Object of class "logical" ~~

groupField:

Object of class "logical" ~~

obsoletes:

Object of class "logical" ~~

local:

Object of class "character" ~~

childrenOf:

Object of class "character" ~~

rows:

Object of class "integer" ~~

start:

Object of class "integer" ~~

url:

Object of class "character" ~~

numFound:

Object of class "integer" ~~

response:

Object of class "data.frame" ~~

Methods and functions

coerce

signature(from = "OlsSearch", to = "data.frame"): ...

coerce

signature(from = "OlsSearch", to = "Terms"): ...

show

signature(object = "OlsSearch"): ...

olsRows

signature(object = "OlsSearch"): ... The value can be updated with the olsRows replacement method. To request all responses, use allRows.

Author(s)

Laurent Gatto <[e-mail]>

Examples

OlsSearch(q = "trans-golgi")
OlsSearch(q = "cell")
OlsSearch(q = "cell", exact = TRUE)
OlsSearch(q = "cell", exact = TRUE, ontology = "go")
OlsSearch(q = "cell", exact = TRUE, ontology = "GO")

OlsSearch(q = "electrospray", ontology = "MS")
OlsSearch(q = "ionization", ontology = "MS")
OlsSearch(q = "electrospray ionization", ontology = "MS")
OlsSearch(q = "electrospray ionization", ontology = "MS", exact=TRUE)

## Request 5 results instead of 20 (default)
OlsSearch(q = "plasma,membrane", ontology = "go", rows = 5)

## or, once the object was created
(res <- OlsSearch(q = "plasma,membrane", ontology = "go"))
olsRows(res) <- 5
res
## all results
res <- allRows(res)
res

res <- OlsSearch(q = "trans-golgi", ontology = "go", rows = 5)
res
res <- olsSearch(res)
res
as(res, "data.frame")
res <- as(res, "Terms")
res
termPrefix(res)
termId(res)

rols documentation built on April 1, 2021, 6:01 p.m.