Summarization methods to get insights into a MoleculeExperiment object

The following methods are useful to get quick view of the contents in a MoleculeExperiment object. For example, showMolecules and showBoundaries summarise the large nested ME list of lists in the molecules and boundaries slots. nFeatures and nTranscripts get the numbers of features or transcripts, respectively.

Usage

# S4 method for MoleculeExperiment
show(object)

# S4 method for MoleculeExperiment
showMolecules(object)

# S4 method for MoleculeExperiment
showBoundaries(object)

# S4 method for MoleculeExperiment
extent(object, assayName = NULL)

# S4 method for MoleculeExperiment
nFeatures(object)

# S4 method for MoleculeExperiment
nTranscripts(object)

Arguments

object: Name of MoleculeExperiment object of interest.
assayName: Character string specifying the name of the assay from which to view a summary of the contents.

Value

A MoleculeExperiment object summary.

Examples

# get example data
repoDir <- system.file("extdata", package = "MoleculeExperiment")
repoDir <- paste0(repoDir, "/xenium_V1_FF_Mouse_Brain")
me <- readXenium(repoDir,
    keepCols = "essential",
    addBoundaries = "cell"
)

showMolecules(me)
#> List of 1
#>  $ detected:List of 2
#>   ..$ sample1:List of 137
#>   .. ..$ 2010300C02Rik        : tibble [11 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ Acsbg1               : tibble [6 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. .. [list output truncated]
#>   ..$ sample2:List of 143
#>   .. ..$ 2010300C02Rik: tibble [9 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ Acsbg1       : tibble [10 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. .. [list output truncated]
showBoundaries(me)
#> List of 1
#>  $ cell:List of 2
#>   ..$ sample1:List of 5
#>   .. ..$ 67500: tibble [13 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ 67512: tibble [13 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. .. [list output truncated]
#>   ..$ sample2:List of 9
#>   .. ..$ 65043: tibble [13 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ 65044: tibble [13 × 2] (S3: tbl_df/tbl/data.frame)
#>   .. .. [list output truncated]

nFeatures(me)
#> - assay detected : 
#> sample1 : 137 
#> sample2 : 143 

nTranscripts(me)
#> - assay detected : 
#> sample1 : 962 
#> sample2 : 777