Class "OlsSearch"

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 <lg390@cam.ac.uk>

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)