numDetectedAcrossFeatures: Number of detected expression values per group of features

In scuttle: Single-Cell RNA-Seq Analysis Utilities

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])

scuttle documentation built on Dec. 19, 2020, 2 a.m.