AssayLinks {QFeatures} | R Documentation

## Links between Assays

### Description

Links between assays within a QFeatures object are handled by an `AssayLinks` object. It is composed by a list of `AssayLink` instances.

### Usage

    ## S4 method for signature 'AssayLink'
    show(object)

    AssayLink(name, from = NA_character_, fcol = NA_character_, hits = Hits())

    AssayLinks(..., names = NULL)

    assayLink(x, i)

    assayLinks(x, i)

    ## S4 method for signature 'AssayLink,character,ANY,ANY'
    x[i, j, ..., drop = TRUE]

    ## S4 method for signature 'AssayLinks,list,ANY,ANY'
    x[i, j, ..., drop = TRUE]

    addAssayLink(object, from, to, varFrom, varTo)

    addAssayLinkOneToOne(object, from, to)

### Arguments

`object` | An `AssayLink` object to show.
`name` | A mandatory name of the assay(s).
`from` | A `character()` or `integer()` indicating which assay(s) to link from in `object`
`fcol` | The feature variable of the parent assay used to generate the current assay (used in `aggregateFeatures`). `NA_character_`, if not applicable.
`hits` | An object of class S4Vectors::Hits matching the features of two assays.
`...` | A set of `AssayLink` objects or a list thereof.
`names` | A `character()` of `AssayLink` names. If provided, `...` are ignored, and `names` is used to create an `AssayLinks` object with `AssayLink` instances with names `names`.
`x` | An instance of class QFeatures.
`i` | The index or name of the assay whose `AssayLink` and parents `AssayLink` instances are to be returned. For `[`, the feature names to filter on.
`j` | ignored.
`drop` | ignored.
`to` | A `character(1)` or `integer(1)` indicating which assay to link to in `object`
`varFrom` | A `character()` indicating the feature variable(s) to use to match the `from` assay(s) to the `to` assay. `varFrom` must have the same length as `from` and is assumed to be ordered as `from`.
`varTo` | A `character(1)` indicating the feature variable to use to match the `to` assay to the `from` assay(s).

### Value

`assayLink` returns an instance of class `AssayLink`.

`assayLinks` returns an instance of class `AssayLinks`.

### Constructors

Object can be created with the `AssayLink()` and `AssayLinks()` constructors.

### Methods and functions

- `assayLink(x, i)` accesses the AssayLink at position `i` or with name `i` in the QFeatures object `x`.

- `parentAssayLinks(x, i, recursive = FALSE)` accesses the parent(s) `AssayLinks` or assay with index or name `i`.

### Creating links between assays

- `addAssayLink` takes a parent assay and a child assay contained in the QFeatures object and creates a link given a matching feature variable in each assay's `rowData`. `addAssayLink` also allows to link an assay from multiple parent assays (see Examples).

- `addAssayLinkOneToOne` links two assays contained in the QFeatures object. The parent assay and the child assay must have the same size and contain the same rownames (a different ordering is allowed). The matching is performed based on the row names of the assays, instead of a supplied variable name in `rowData`. Providing multiple parents is not supported.

### Examples

    ##-----------------------------
    ## Creating an AssayLink object
    ##-----------------------------

    al1 <- AssayLink(name = "assay1")
    al1

    ##------------------------------
    ## Creating an AssayLinks object
    ##------------------------------

    AssayLinks(al1)

    al2 <- AssayLinks(names = c("Assay1", "Assay2"))
    al2

    ##---------------------------------------
    ## Adding an AssayLink between two assays
    ##---------------------------------------

    ## create a QFeatures object with 2 (identical) assays
    ## see also '?QFeatures'
    se <- SummarizedExperiment(matrix(runif(20), ncol = 2,
                                      dimnames = list(LETTERS[1:10],
                                                      letters[1:2])),
                               rowData = DataFrame(ID = 1:10))
    ft <- QFeatures(list(assay1 = se, assay2 = se))

    ## assay1 and assay2 are not linked
    assayLink(ft, "assay2") ## 'from' is NA
    assayLink(ft, "assay1") ## 'from' is NA

    ## Suppose assay2 was generated from assay1 and the feature variable
    ## 'ID' keeps track of the relationship between the two assays
    ftLinked <- addAssayLink(ft, from = "assay1", to = "assay2",
                             varFrom = "ID", varTo = "ID")
    assayLink(ftLinked, "assay2")

    ## For one-to-one relationships, you can also use
    ftLinked <- addAssayLinkOneToOne(ft, from = "assay1", to = "assay2")
    assayLink(ftLinked, "assay2")

    ##----------------------------------------
    ## Adding an AssayLink between more assays
    ##----------------------------------------

    ## An assay can also be linked to multiple parent assays
    ## Create a QFeatures object with 2 parent assays and 1 child assay
    ft <- QFeatures(list(parent1 = se[1:6, ], parent2 = se[4:10, ], child = se))
    ft <- addAssayLink(ft, from = c("parent1", "parent2"), to = "child",
                       varFrom = c("ID", "ID"), varTo = "ID")
    assayLink(ft, "child")

[Package QFeatures version 1.2.0 Index]