ContactMatrix-accessors: ContactMatrix accessors

In LTLA/InteractionSet: Base Classes for Storing Genomic Interaction Data

ContactMatrix accessors

Description

Methods to get and set fields in an ContactMatrix object.

Usage

## S4 method for signature 'ContactMatrix'
anchors(x, type="both", id=FALSE)
## S4 method for signature 'ContactMatrix'
anchorIds(x, type="both")
## S4 replacement method for signature 'ContactMatrix'
anchorIds(x, type="both") <- value

## S4 method for signature 'ContactMatrix'
regions(x)
## S4 replacement method for signature 'ContactMatrix'
regions(x) <- value
## S4 replacement method for signature 'ContactMatrix'
replaceRegions(x) <- value
## S4 replacement method for signature 'ContactMatrix'
appendRegions(x) <- value
## S4 method for signature 'ContactMatrix'
reduceRegions(x)

## S4 method for signature 'ContactMatrix'
show(x)
## S4 method for signature 'ContactMatrix'
as.matrix(x)
## S4 replacement method for signature 'ContactMatrix'
as.matrix(x) <- value
## S4 method for signature 'ContactMatrix'
t(x)

## S4 method for signature 'ContactMatrix'
dim(x)
## S4 method for signature 'ContactMatrix'
dimnames(x)
## S4 replacement method for signature 'ContactMatrix'
dimnames(x) <- value
## S4 method for signature 'ContactMatrix'
length(x)

Arguments

x	A ContactMatrix object.
type	a string specifying which anchors are to be extracted or replaced.
id	a scalar logical indicating whether indices or GRanges should be returned.
value	For anchorIds<-, a list of two integer vectors when type="both". The first and second vectors must have length equal to the number of rows and columns of x, respectively. For type="row" or "column", only one vector needs to be supplied corresponding to either the rows or columns. For regions<-, a GRanges object of length equal to that of regions(x). For newRegions<-, a GRanges object that is a superset of all entries in regions(x) involved in interactions. For appendRegions<-, a GRanges of any length containing additional regions. For as.matrix<-, a matrix-like object of the same dimensions as that in the matrix slot. For dimnames<-, a list of two character vectors corresponding to the row and column names, respectively. These can also be passed separately via rownames<- and colnames<-.

Details

The return value of anchors varies depending on type and id:

• If id=FALSE, a GRanges object is returned containing the regions specified by the anchor1 or anchor2 slots in x, for type=="row" or "column", respectively.

• If id=FALSE and type="both", a list is returned with two entries row and column, containing regions specified by anchor1 and anchor2 respectively.

• If id=TRUE, the integer vectors in the anchor1 or anchor2 slots of x are returned directly, depending on type. A list of length two is returned for type="both", containing both of these vectors.

Note that anchorIds is equivalent to calling anchors with id=TRUE.

Replacement in anchorIds<- can only be performed using anchor indices. If type="both", a list of two integer vectors is required in value, specifying the indices of the row- and column-wise interacting regions in x. If type="row" or "column", an integer vector is required to replace the existing row- or column-wise indices in the anchor1 or anchor2 slot, respectively.

For regions, a GRanges is returned equal to the regions slot in x. For regions<-, the GRanges in value is used to replace the regions slot. Resorting of the replacement GRanges is performed automatically, along with re-indexing of the anchors. In addition, the input GRanges must be of the same length as the existing object in the regions slot. The newRegions replacement method can take variable length GRanges, but requires that the replacement contain (at least) all ranges contained in anchors(x). The appendRegions replacement method appends extra intervals to the existing regions slot of x. The reduceRegions method removes unused entries in the regions slot, to save memory – see reduceRegions,GInteractions-method for more details.

The show method will print out various details of the object, such as the dimensions of the matrix slot and the length of the regions slot. The as.matrix method will return the value of the matrix slot, containing a matrix-like object of interaction data. Replacement with a matrix-like object of the same dimensions can be performed using the as.matrix<- function. The t method will transpose the matrix, i.e., switch the rows and columns (and switch the vectors in the anchor1 and anchor2 slots).

The dim method will return a vector of length 2, containing the dimensions of the matrix slot. The dimnames method will return a list of length 2, containing the row and column names of matrix (these can be modified with the dimnames<- method). The length method will return an integer scalar corresponding to the total number of entries in the matrix slot.

As the ContactMatrix class inherits from the Annotated class, additional metadata can be stored in the metadata slot. This can be accessed or modified with metadata,Annotated-method.

Value

For the getters, values in various slots of x are returned, while for the setters, the slots of x are modified accordingly – see Details.

Author(s)

Aaron Lun

See Also

ContactMatrix-class

Examples

example(ContactMatrix, echo=FALSE) # Generate a nice object.
show(x)

# Various matrix methods:
as.matrix(x)
t(x)

nrow(x)
ncol(x)
length(x)

# Accessing anchor ranges or indices:
anchors(x)
anchors(x, type="row")
anchors(x, id=TRUE)

anchors(x, id=TRUE, type="row")
anchors(x, id=TRUE, type="column")

# Modifying anchor indices:
nregs <- length(regions(x))
anchorIds(x) <- list(sample(nregs, nrow(x), replace=TRUE),
                   sample(nregs, ncol(x), replace=TRUE))
anchors(x, id=TRUE, type="row")
anchors(x, id=TRUE, type="column")

# Accessing or modifying regions:
regions(x)
regions(x)$score <- runif(length(regions(x)))

new.ranges <- c(regions(x), resize(regions(x), fix="center", width=50))
try(regions(x) <- new.ranges) # Fails
replaceRegions(x) <- new.ranges # Succeeds

length(regions(x))
appendRegions(x) <- GRanges("chrA", IRanges(5:10+1000, 1100+5:10), score=runif(6))
length(regions(x))

reduceRegions(x)

# Setting metadata
metadata(x)$name <- "I am a contact matrix"
metadata(x)

LTLA/InteractionSet documentation built on July 3, 2023, 8:44 a.m.