aggregateAcrossFeatures {scuttle} | R Documentation

## Aggregate feature sets in a SummarizedExperiment

### Description

Sum together expression values (by default, counts) for each feature set in each cell of a SummarizedExperiment object.

### Usage

    aggregateAcrossFeatures(
      x,
      ids,
      ...,
      use.assay.type = "counts",
      use_exprs_values = NULL
    )

### Arguments

`x` | A SummarizedExperiment containing an expression matrix.
`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.
`...` | Further arguments to be passed to `sumCountsAcrossFeatures`.
`use.assay.type` | A character or integer vector specifying the assay(s) of `x` containing expression matrices.
`use_exprs_values` | Soft-deprecated equivalent of `use.assay.type`.

### Value

A SummarizedExperiment of the same class as `x` is returned, containing summed matrices generated by `sumCountsAcrossFeatures` on all assays in `use.assay.type`.

If `ids` is a factor, row metadata is retained for the first instance of a feature from each set in `ids`. This behavior assumes that `ids` specifies duplicates of the same gene, such that the first instance is a reasonable choice.

If `ids` is a list, row metadata is simply discarded. This behavior assumes that `ids` specifies gene sets such that any existing gene-level metadata is meaningless.

### Author(s)

Aaron Lun

### See Also

`sumCountsAcrossFeatures`, which does the heavy lifting.

### Examples

    example_sce <- mockSCE()
    ids <- sample(LETTERS, nrow(example_sce), replace=TRUE)
    aggr <- aggregateAcrossFeatures(example_sce, ids)
    aggr

[Package scuttle version 1.4.0 Index]