Links between Assays — AssayLinks • QFeatures

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

# S4 method for AssayLink
show(object)

# S4 method for AssayLinks
updateObject(object, ..., verbose = FALSE)

# S4 method for AssayLink
updateObject(object, ..., verbose = FALSE)

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

AssayLinks(..., names = NULL)

assayLink(x, i)

assayLinks(x, i)

# S4 method for AssayLink,character,ANY,ANY
[(x, i, j, ..., drop = TRUE)

# S4 method for 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.
...: A set of AssayLink objects or a list thereof.
verbose: logical (default FALSE) whether to print extra messages
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.
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 below).
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
#> AssayLink for assay <assay1>
#> [from:NA|fcol:NA|hits:0]

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

AssayLinks(al1)
#> AssayLinks of length 1
#> names(1): assay1

al2 <- AssayLinks(names = c("Assay1", "Assay2"))
al2
#> AssayLinks of length 2
#> names(2): Assay1 Assay2

##---------------------------------------
## 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 for assay <assay2>
#> [from:NA|fcol:NA|hits:0]
assayLink(ft, "assay1") ## 'from' is NA
#> AssayLink for assay <assay1>
#> [from:NA|fcol:NA|hits:0]

## 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")
#> AssayLink for assay <assay2>
#> [from:assay1|fcol:ID|hits:10]

## For one-to-one relationships, you can also use
ftLinked <- addAssayLinkOneToOne(ft, from = "assay1", to = "assay2")
assayLink(ftLinked, "assay2")
#> AssayLink for assay <assay2>
#> [from:assay1|fcol:._oneToOne|hits:10]

##----------------------------------------
## 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")
#> AssayLink for assay <child>
#> [from:parent1,parent2|fcol:ID,ID|hits:6,7]