Extract data from a SingleCellExperiment object — sce_extract • Single Cell Pathway Analysis (SCPA)

This function takes a SingleCellExperiment object as an input, and returns an expression matrix based on subsetting parameters. Either none, one, or two metadata features can be selected for a given input.

sce_extract(
  sce_object,
  assay_name = "logcounts",
  meta1 = NULL,
  value_meta1 = NULL,
  meta2 = NULL,
  value_meta2 = NULL,
  pseudocount = 0.001
)

Arguments

sce_object: SingleCellExperiment object containing expression data
assay_name: Name of assay to pull from. Defaults to "logcounts"
meta1: Metadata column to subset
value_meta1: Value to select within meta1 column
meta2: Metadata column to subset
value_meta2: Value to select within meta2 column
pseudocount: Pseudocount to add to data. Defaults to 0.001

Value

Matrix containing count values of selected populations

Examples

if (FALSE) {
cd4 <- sce_extract(
   sce_object,
   meta1 = "Hour",
   value_meta1 = 12,
   meta2 = "Cell_Type",
   value_meta2 = "CD4"
)
}