setQuery {InterMineR} | R Documentation

## Initialize a new InterMineR query or modify an existing list query

### Description

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.

### Usage

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

### Arguments

`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'.

### Details

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.

### Value

An InterMineR object

### Author(s)

InterMine Team

### See Also

`setConstraints`, `runQuery`, `InterMineR-class`

### Examples

    # 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

[Package InterMineR version 1.10.0 Index]