setQuery: Initialize a new InterMineR query or modify an existing list...
In intermine/InterMineR: R Interface with InterMine-Powered Databases

Description Usage Arguments Details Value Author(s) See Also Examples

setQuery function is used to create a query for an InterMine instance. It can also accept and modify pre-defined queries of class list, like the template queries which can be retrieved with the function getTemplateQuery. It returns a defined query stored as an object of class 'InterMineR'.

A query needs to have at least view, constraints and constraintLogic. The view is a vector containing the columns of the query output. The constraint is a matrix containing the following columns: path (the path of the constraint), op (the constraint operator, one of '=', '!=', 'LOOKUP', 'ONE OF', 'NONE OF', '>', '<', '>=', '<=', 'LIKE'), value (the constraint value), code (the name of the constraint), extraValue (optional, required for LOOKUP constraints). The constraintLogic by default is "AND" operation, e.g., "A and B", where A and B are the codes in the constraints.

setQuery(
  select,
  orderBy,
  where,
  name = "",
  description = "",
  inheritQuery
)

`select`	a character vector defining the type of data to be returned.
`orderBy`	a list the name of the column and the type of sorting which will be used to order the retrieved data.frame.
`where`	a list containing the constraints used to restrict the query. Each constraint constitutes a list as well. If one wishes for a single constraint to possess more than one values, the `setConstraints` function can be used.
`name`	Assign with a character string giving a name to the query. Pre-fixed with "".
`description`	Assign with a character string describing the purpose and the type of data retrieved by the query. Pre-fixed with "".
`inheritQuery`	Assign with a pre-defined query list, the input values of which can be modified and inherited in the new query object of class 'InterMineR'.

setQuery function can be used to create queries with a single constraint containing multiple values. The constraints can be first defined with the setConstraints function. The resulting 'InterMineR' object is passed to the runQuery function to perform the query.

An InterMineR object

InterMine Team

setConstraints, runQuery, InterMineR-class

# get mine 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
)

class(go.query)
go.query

# 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
)

class(hsa.go.query)
hsa.go.query