Select samples

Utility function that enables quick and easy sample selection.

Usage

selectSamples(object, ...)

# S4 method for SingleCellExperiment
selectSamples(object, ...)

Arguments

object

Object.

...

Selection arguments:

Key value pairs that must map to the column names of sampleData().
atomic values are supported.
Avoid using logical or numeric indices (e.g. which() return), thereby making your code more human readable, and easier to interpret.

Value

Modified object. Subset (extraction) containing the desired samples.

Details

Internally, pattern matching against sample and file names is applied using logical grep matching.

Note

Updated 2022-03-02.

Intended usage

This function is intended to be used for sample extraction from Bioconductor container classes where the column names don't correspond to samples (e.g. SingleCellExperiment).

Bracket-based subsetting

Bracket-based subsetting with [ also works on SingleCellExperiment objects but it's not intuitive. In this case, provide cellular barcode identifiers for columns and gene identifiers for rows.

Examples

data(SingleCellExperiment_splatter, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
sample <- Biobase::sampleNames(object)[[1L]]
print(sample)
#> [1] "sample3"
subset <- selectSamples(object, sampleName = sample)
#> ℹ 1 sample matched: "sample3".
#> ℹ 121 cells matched.
print(subset)
#> class: SingleCellExperiment 
#> dim: 100 121 
#> metadata(2): date selectSamples
#> assays(1): counts
#> rownames(100): gene001 gene002 ... gene099 gene100
#> rowData names(10): broadClass description ... ncbiGeneId seqCoordSystem
#> colnames(121): cell001 cell002 ... cell398 cell399
#> colData names(1): sampleId
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):