numDetectedAcrossCells {scuttle} | R Documentation

## Number of detected expression values per group of cells

### Description

Computes the number of detected expression values (by default, defined as non-zero counts) for each feature in each group of cells. This function is deprecated: use `summarizeAssayByGroup` instead.

### Usage

    numDetectedAcrossCells(x, ...)

    ## S4 method for signature 'ANY'
    numDetectedAcrossCells(
      x,
      ids,
      subset.row = NULL,
      subset.col = NULL,
      store.number = "ncells",
      average = FALSE,
      threshold = 0,
      BPPARAM = SerialParam(),
      subset_row = NULL,
      subset_col = NULL,
      store_number = NULL,
      detection_limit = NULL
    )

    ## S4 method for signature 'SummarizedExperiment'
    numDetectedAcrossCells(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 specifying the group to which each cell in `x` belongs. Alternatively, a DataFrame of such vectors or factors, in which case each unique combination of levels defines a group.
`subset.row` | An integer, logical or character vector specifying the features to use. If `NULL`, defaults to all features. For the SingleCellExperiment method, this argument will not affect alternative Experiments, where aggregation is always performed for all features (or not at all, depending on `use_alt_exps`).
`subset.col` | An integer, logical or character vector specifying the cells to use. Defaults to all cells with non-`NA` entries of `ids`.
`store.number` | String specifying the field of the output `colData` to store the number of cells in each group. If `NULL`, nothing is stored.
`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 to the arguments described above.
`subset_col` | Soft-deprecated equivalents to the arguments described above.
`store_number` | Soft-deprecated equivalents to 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

A SummarizedExperiment is returned containing a count matrix in the first assay. Each column corresponds to group as defined by a unique level or combination of levels in `ids`. Each entry of the matrix contains the number of cells with detected expression for a feature and group. The identities of the levels for each column are reported in the `colData`. If `average=TRUE`, the assay is instead a numeric matrix containing the proportion of detected values.

### Author(s)

Aaron Lun

### See Also

`sumCountsAcrossCells`, which computes the sum of counts within a group.

### Examples

    example_sce <- mockSCE()

    ids <- sample(LETTERS[1:5], ncol(example_sce), replace=TRUE)
    bycol <- numDetectedAcrossCells(example_sce, ids)
    head(bycol)

[Package scuttle version 1.4.0 Index]