calcIsExprs {scater} | R Documentation |
Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels.
calcIsExprs(object, lowerDetectionLimit = 0, exprs_values = "counts")
object |
a |
lowerDetectionLimit |
numeric scalar giving the minimum expression level for an expression observation in a cell for it to qualify as expressed. |
exprs_values |
character scalar indicating whether the count data
( |
a logical matrix indicating whether or not a feature in a particular cell is expressed.
data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) assay(example_sce, "is_exprs") <- calcIsExprs(example_sce, lowerDetectionLimit = 1, exprs_values = "counts")