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.

Description

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.

Usage

calcIsExprs(object, detection_limit = 0, exprs_values = "counts")

Arguments

object

a SingleCellExperiment object with expression and/or count data.

detection_limit

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 ("counts"), the log-transformed count data ("logcounts"), transcript-per-million ("tpm"), counts-per-million ("cpm") or FPKM ("fpkm") should be used to define if an observation is expressed or not. Defaults to the first available value of those options in the order shown.

Value

a logical matrix indicating whether or not a feature in a particular cell is expressed.

Examples

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, 
detection_limit = 1, exprs_values = "counts")

[Package scater version 1.10.1 Index]