nexprs {scater} | R Documentation

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

### Description

Counting the number of non-zero counts in each row (per feature) or column (per cell), without constructing an intermediate logical matrix.

### Usage

    nexprs(x, ...)

    ## S4 method for signature 'ANY'
    nexprs(x, byrow = FALSE, detection_limit = 0,
      subset_row = NULL, subset_col = NULL, BPPARAM = SerialParam())

    ## S4 method for signature 'SummarizedExperiment'
    nexprs(x, ..., exprs_values = "counts")

### Arguments

`x` | A numeric matrix of counts where features are rows and cells are columns. Alternatively, a SummarizedExperiment containing such counts.
`...` | For the generic, further arguments to pass to specific methods. For the SummarizedExperiment method, further arguments to pass to the ANY method.
`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.
`detection_limit` | Numeric scalar providing the value above which observations are deemed to be expressed.
`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.
`exprs_values` | String or integer specifying the assay of `x` to obtain the count matrix from.

### Value

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

### Author(s)

Aaron Lun

### See Also

`numDetectedAcrossFeatures` and `numDetectedAcrossCells`, to do this calculation for each group of features or cells, respectively.

### Examples

    example_sce <- mockSCE()

    nexprs(example_sce)[1:10]
    nexprs(example_sce, byrow = TRUE)[1:10]

[Package scater version 1.14.0 Index]