Create scMetaLink from SingleCellExperiment

Initialize a scMetaLink object from a SingleCellExperiment object

createScMetaLinkFromSCE(
  sce,
  cell_type_column = "cell_type",
  assay_name = "logcounts",
  min_cells = 10
)

Arguments

sce

A SingleCellExperiment object

cell_type_column

Character. Column name in colData for cell type annotations

assay_name

Character. Name of assay to use (default: "logcounts")

min_cells

Integer. Minimum cells per cell type

Value

A scMetaLink object

Examples

# \donttest{
if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
  library(SingleCellExperiment)
  # Create example SCE
  counts <- matrix(rpois(1000, 5), nrow = 100, ncol = 10)
  rownames(counts) <- paste0("Gene", 1:100)
  colnames(counts) <- paste0("Cell", 1:10)
  sce <- SingleCellExperiment(assays = list(counts = counts, logcounts = log1p(counts)))
  colData(sce)$cell_type <- rep(c("TypeA", "TypeB"), each = 5)
  # obj <- createScMetaLinkFromSCE(sce, "cell_type")
}
#> Loading required package: SummarizedExperiment
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#> 
#> Attaching package: ‘MatrixGenerics’
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#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
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#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
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#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
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# }