runQuery {InterMineR} | R Documentation |
Returns results from a query against data held inside the mine. These queries are similar to SQL queries, in that they request certain defined output columns of output, filtering the results through a series of "constraints".
runQuery(im, qry, timeout = 60)
im |
a list, containing the base URL and API token. |
qry |
an InterMineR or a list object, representing the query to the database. |
timeout |
an integer, representing the number of seconds to wait for the web service to respond. |
Use setQuery
function to create an InterMineR object. For setting a single constraint with multiple values, the function setConstraints
can be used.
Alternatively, the user can define manually the constraints, the selection of data to be returned and the value by which they are ordered, as a list object.
For more information checkout the vignette of the package.
a data.frame containing the data which were retrieved from the InterMine instance.
# S4 method for class 'InterMineR'
runQuery(im, qry = "InterMineR")
The method accepts an object of the class InterMineR and uses its information to perform the query on the defined InterMine instance.
InterMineR-class
objects can contain a single constraint with multiple values.
# S4 method for class 'list'
runQuery(im, qry = "list")
The method accepts an object of the class list and uses its information to perform the query on the defined InterMine instance.
Queries defined as lists can possess only constraints with one value.
InterMine Team
setConstraints
, setQuery
, InterMineR-class
, newQuery
# 1. Adapt 'GO_Gene' template query from FlyMine to 'InterMineR' # get FlyMine instance im.fly = initInterMine(listMines()["FlyMine"]) # get GO_Gene template query qGO_Gene = getTemplateQuery(im.fly, "GO_Gene") # constraint with GO value qGO_Gene$where[[3]] # modify GO_Gene template query to have more than one GO values go.constraints = setConstraints( values = list(c("DNA repair", "cellular response to DNA damage stimulus")), modifyQueryConstraints = qGO_Gene, m.index = 3 ) go.constraints[[3]] # create 'InterMineR' object go.query = setQuery( inheritQuery = qGO_Gene, where = go.constraints ) go.query # run InterMineR query go.results = runQuery( im = im.fly, qry = go.query ) head(go.results) # 2. Create similar query manually for Homo sapiens, using HumanMine # get HumanMine instance im.human = initInterMine(listMines()["HumanMine"]) # create constraints using GO terms and organism as values hsa.go.constraints = setConstraints( paths = c("Gene.goAnnotation.ontologyTerm.parents.name", "Gene.organism.name"), operators = rep("=", 2), values = list(c("DNA repair", "cellular response to DNA damage stimulus"), "Homo sapiens") ) hsa.go.constraints # create 'InterMineR' object hsa.go.query = setQuery( select = c("Gene.secondaryIdentifier", "Gene.symbol", "Gene.goAnnotation.ontologyTerm.parents.name", "Gene.goAnnotation.ontologyTerm.parents.identifier", "Gene.goAnnotation.ontologyTerm.name", "Gene.goAnnotation.ontologyTerm.identifier"), orderBy = list(c(Gene.secondaryIdentifier = "ASC")), where = hsa.go.constraints ) hsa.go.query # run InterMineR query hsa.go.results = runQuery( im = im.human, qry = hsa.go.query ) head(hsa.go.results)