LoomExperiment-class: LoomExperiment, RangedLoomExperiment, and...

In Bioconductor/LoomExperiment: LoomExperiment container

LoomExperiment, RangedLoomExperiment, and SingleCellLoomExperiment classes

Description

The LoomExperiment family of classes is used as a bridge between Bioconductor's "Experiment" classes and the Linnarson Lab's http://linnarssonlab.org/loompy/index.html. The family of LoomExperiment classes all inherit from the class LoomExperiment as well as their respectively named parent classes. The LoomExperiment class inheirts from SummarizedExperiment.

Usage

## Constructor

LoomExperiment(..., colGraphs = LoomGraphs(), rowGraphs = LoomGraphs())
RangedLoomExperiment(..., colGraphs = LoomGraphs(), rowGraphs = LoomGraphs())
SingleCellLoomExperiment(..., colGraphs = LoomGraphs(), rowGraphs = LoomGraphs())

## Accessors

## S4 method for signature 'LoomExperiment'
colGraphs(x, ...)
## S4 replacement method for signature 'LoomExperiment'
colGraphs(x, ...) <- value
## S4 method for signature 'LoomExperiment'
rowGraphs(x, ...)
## S4 replacement method for signature 'LoomExperiment'
rowGraphs(x, ...) <- value

## Subsetting

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

## Binding

## S4 method for signature 'LoomExperiment'
rbind(..., deparse.level=1)
## S4 method for signature 'LoomExperiment'
cbind(..., deparse.level=1)

Arguments

x	A LoomExperiment object
colGraphs, rowGraphs	LoomGraphs to be placed in either the colGraphs or rowGraphs slot respectively
value	For colGraphs<- and rowGraphs<-, value will be the replacement to the slot. For dropHits<-, indices to replace selected indices with.
...	For constructors, ... will be passed on to the respective Experiment constructor.
i, j	For subsetting, indices specifying elements to subset LoomGraph by. For dropHits, numeric indicating the node number
drop	For matrices and arrays. If 'TRUE' the result is coerced to the lowest posible dimesnion. This only woeks for extracting elements, not for the replacement.
deparse.level	See '?base::cbind' for a description of this argument.

Details

The LoomExperiment class is a virtual class meant to to act as an interface for other "_LoomExperiment" classes. It contains two slots:

colGraphs:

A LoomGraphs object containing col_graph data as specified by the loom format.

rowGraphs:

A LoomGraphs object containing row_graph data as specified by the loom format.

The intended use of this class is as an interface that allows various slots and operations necessary for subsequent "_LoomExperiment" classes to be defined.

The colGraphs and rowGraphs slot stores a LoomGraphs object that stores a graph of edges between vertices and possibly associated weights. These slots may be NULL.

Value

An object of class LoomExperiment

Author(s)

Daniel Van Twisk

See Also

SummarizedExperiment, RangedSummarizedExperiment, SingleCellExperiment

Examples

## Construction
counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
sce <- SingleCellExperiment(assays = list(counts = counts))
scle <- SingleCellLoomExperiment(sce)
# OR
scle <- SingleCellLoomExperiment(assays = list(counts = counts))
# OR
scle <- as(sce, "SingleCellLoomExperiment")
scle

## Get and replace rowGraphs and colGraphs
colGraphs(scle)
rowGraphs(scle)

a <- c(1, 2, 3)
b <- c(3, 2, 1)
w <- c(100, 10, 1)
lg <- LoomGraph(a, b, weight=w)
lgs <- LoomGraphs(lg, lg)
names(lgs) <- c('lg1', 'lg2')
lgs

colGraphs(scle) <- lgs
rowGraphs(scle) <- lgs

colGraphs(scle)
rowGraphs(scle)
colGraphs(scle)[[1]]
rowGraphs(scle)[[1]]

## Subsetting
scle2 <- scle[c(1, 3), 1:2]
colGraphs(scle2)[[1]]
rowGraphs(scle2)[[1]]

Bioconductor/LoomExperiment documentation built on Nov. 2, 2024, 9:57 p.m.