Description Usage Arguments Value Author(s) See Also Examples

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
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)
``` |

`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 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- |

`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 |

`exprs_values, detection_limit` |
Soft-deprecated equivalents of the arguments above. |

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.

Aaron Lun

`sumCountsAcrossFeatures`

, on which this function is based.

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