LoomExperiment {LoomExperiment} | R Documentation |
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
.
## 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)
x |
A LoomExperiment object |
colGraphs,rowGraphs |
LoomGraphs to be placed in either the colGraphs or rowGraphs slot respectively |
value |
For |
... |
For constructors, |
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. |
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
.
An object of class LoomExperiment
Daniel Van Twisk
SummarizedExperiment
,
RangedSummarizedExperiment
,
SingleCellExperiment
## 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]]