nexprs {scater}R Documentation

Count the number of expressed genes per cell

Description

An efficient internal function that avoids the need to construct 'is_exprs_mat' by counting the number of expressed genes per cell on the fly.

Usage

nexprs(object, detection_limit = 0, exprs_values = "counts",
  byrow = FALSE, subset_row = NULL, subset_col = NULL)

Arguments

object

a SingleCellExperiment object or a numeric matrix of expression values.

detection_limit

numeric scalar providing the value above which observations are deemed to be expressed. Defaults to object@detection_limit.

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. However, if is_exprs(object) is present, it will be used directly; exprs_values and detection_limit are ignored.

byrow

logical scalar indicating if TRUE to count expressing cells per feature (i.e. gene) and if FALSE to count expressing features (i.e. genes) per cell.

subset_row

logical, integeror character vector indicating which rows (i.e. features/genes) to use.

subset_col

logical, integer or character vector indicating which columns (i.e., cells) to use.

Details

Setting subset_row or subset_col is equivalent to subsetting object before calling nexprs, but more efficient as a new copy of the matrix is not constructed.

Value

If byrow=TRUE, an integer vector containing the number of cells expressing each feature, of the same length as the number of features in subset_row (all features in exprs_mat if subset_row=NULL).

If byrow=FALSE, an integer vector containing the number of genes expressed in each cell, of the same length as the number of cells specified in subset_col (all cells in exprs_mat if subset_col=NULL).

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sce <- SingleCellExperiment(
assays = list(counts = sc_example_counts), colData = sc_example_cell_info)
nexprs(example_sce)[1:10]
nexprs(example_sce, byrow = TRUE)[1:10]
[Package scater version 1.8.4 Index]