numDetectedAcrossFeatures {scuttle} | R Documentation

## Number of detected expression values per group of features

### Description

Computes the number of detected expression values (by default, defined as non-zero counts) for each group of features in each cell.

### Usage

    numDetectedAcrossFeatures(x, ...)

    ## S4 method for signature 'ANY'
    numDetectedAcrossFeatures(
      x,
      ids,
      subset.row = NULL,
      subset.col = NULL,
      average = FALSE,
      threshold = 0,
      BPPARAM = SerialParam(),
      subset_row = NULL,
      subset_col = NULL,
      detection_limit = NULL
    )

    ## S4 method for signature 'SummarizedExperiment'
    numDetectedAcrossFeatures(x, ..., assay.type = "counts", exprs_values = NULL)

### Arguments

`x` | A numeric matrix of counts containing features in rows and cells in columns. Alternatively, a SummarizedExperiment object containing such a count matrix.
`...` | For the generic, further arguments to pass to specific methods. For the SummarizedExperiment method, further arguments to pass to the ANY method.
`ids` | A factor of length `nrow(x)`, specifying the set to which each feature in `x` belongs. Alternatively, a list of integer or character vectors, where each vector specifies the indices or names of features in a set. Logical vectors are also supported.
`subset.row` | An integer, logical or character vector specifying the features to use. Defaults to all features.
`subset.col` | An integer, logical or character vector specifying the cells to use. Defaults to all cells with non-`NA` entries of `ids`.
`average` | Logical scalar indicating whether the proportion of non-zero counts in each group should be computed instead.
`threshold` | A numeric scalar specifying the threshold above which a gene is considered to be detected.
`BPPARAM` | A BiocParallelParam object specifying whether summation should be parallelized.
`subset_row` | Soft-deprecated equivalents of the arguments described above.
`subset_col` | Soft-deprecated equivalents of the arguments described above.
`assay.type` | A string or integer scalar specifying the assay of `x` containing the matrix of counts (or any other expression quantity that can be meaningfully summed).
`exprs_values, detection_limit` | Soft-deprecated equivalents of the arguments above.

### Value

An integer matrix containing the number of detected expression values in each group of features (row) and cell (column). If `average=TRUE`, this is instead a numeric matrix containing the proportion of detected values.

### Author(s)

Aaron Lun

### See Also

`sumCountsAcrossFeatures`, on which this function is based.

### Examples

    example_sce <- mockSCE()

    ids <- sample(paste0("GENE_", 1:100), nrow(example_sce), replace=TRUE)
    byrow <- numDetectedAcrossFeatures(example_sce, ids)
    head(byrow[,1:10])

[Package scuttle version 1.4.0 Index]