nexprs {scater} | R Documentation |
Counting the number of non-zero counts in each row (per feature) or column (per cell).
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")
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 |
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.
Only relevant when |
exprs_values |
String or integer specifying the assay of |
An integer vector containing counts per gene or cell, depending on the provided arguments.
Aaron Lun
numDetectedAcrossFeatures
and numDetectedAcrossCells
,
to do this calculation for each group of features or cells, respectively.
example_sce <- mockSCE() nexprs(example_sce)[1:10] nexprs(example_sce, byrow = TRUE)[1:10]