nexprs {scater}R Documentation

Count the number of non-zero counts per cell or feature

Description

An efficient internal function that counts the number of non-zero counts in each row (per feature) or column (per cell). This avoids the need to construct an intermediate logical matrix.

Usage

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

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.

exprs_values

String or integer specifying the assay of object to obtain the count matrix from, if object is a SingleCellExperiment.

byrow

Logical scalar indicating whether to count the number of detected cells per feature. If FALSE, the function will count the number of detected features per cell.

subset_row

Logical, integer or character vector indicating which rows (i.e. features) to use.

subset_col

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

BPPARAM

A BiocParallelParam object specifying whether the calculations should be parallelized.

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

An integer vector containing counts per gene or cell, depending on the provided arguments.

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 1.10.1 Index]