Coercion methods for GraphExperiment objects

The GraphExperiment class inherits from SingleCellExperiment, which in turn inherits from (Ranged)SummarizedExperiment. To ensure GraphExperiment easily interoperates with these classes, we provide users with traditional as() coercion methods.

Arguments

from

An object of class SingleCellExperiment, SummarizedExperiment, or RangedSummarizedExperiment to be coerced to GraphExperiment.

Value

A GraphExperiment object.

Examples

# Simulate a count matrix
gene_ids <- paste0("gene", seq_len(200))
cell_ids <- paste0("cell", seq_len(100))
mat <- matrix(rpois(20000, 5), ncol = 100, dimnames = list(gene_ids, cell_ids))

# Coerce from `SummarizedExperiment`
se <- SummarizedExperiment(assays = list(mat))
as(se, "GraphExperiment")
#> class: GraphExperiment 
#> dim: 200 100 
#> metadata(0):
#> assays(1): ''
#> rownames(200): gene1 gene2 ... gene199 gene200
#> rowData names(0):
#> colnames(100): cell1 cell2 ... cell99 cell100
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowGraphs(0):
#> colGraphs(0):

# Coerce from `RangedSummarizedExperiment`
rse <- as(se, "RangedSummarizedExperiment")
as(rse, "GraphExperiment")
#> class: GraphExperiment 
#> dim: 200 100 
#> metadata(0):
#> assays(1): ''
#> rownames(200): gene1 gene2 ... gene199 gene200
#> rowData names(0):
#> colnames(100): cell1 cell2 ... cell99 cell100
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowGraphs(0):
#> colGraphs(0):

# Coerce from `SingleCellExperiment`
sce <- as(se, "SingleCellExperiment")
as(sce, "GraphExperiment")
#> class: GraphExperiment 
#> dim: 200 100 
#> metadata(0):
#> assays(1): ''
#> rownames(200): gene1 gene2 ... gene199 gene200
#> rowData names(0):
#> colnames(100): cell1 cell2 ... cell99 cell100
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowGraphs(0):
#> colGraphs(0):