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Raw counts from a VISTA object

Source: R/counts-methods.R
counts.Rd

Returns the filtered raw count matrix stored alongside the normalized counts. Objects built before VISTA 1.2.0, or with create_vista(keep_raw_counts = FALSE), do not carry one.

Usage

# S4 method for class 'VISTA'
counts(object, ...)

Arguments

object

A VISTA object.

...

Ignored.

Value

A numeric matrix of raw counts with genes in rows and samples in columns.

Details

Normalized counts are not invertible, so BiocGenerics::updateObject() cannot back-fill this assay for an older object; it has to be rebuilt with create_vista().

Examples

v <- example_vista()
counts(v)[seq_len(3), seq_len(3)]
#>                 SRR1039508 SRR1039512 SRR1039516
#> ENSG00000000003        679        873       1138
#> ENSG00000000419        467        621        587
#> ENSG00000000457        260        263        245