Save the counts matrix as a single table.

Layers left split by a merge() are rejoined first, since LayerData() would otherwise return only the first of them, and warn rather than error while doing it.

Usage

save_counts(x, assay = "RNA", layer = "data", digits = 3, file)

Arguments

x

A Seurat object.

assay

Assay to retrieve the counts from.

layer

Layer to retrieve. The default "data" layer holds the normalized and log-transformed expression used for visualization and most differential expression tests.

digits

Number of digits to round the values to. Ignored for a layer that already holds whole numbers, such as raw counts.

file

Path to write the table to as a csv, or NULL to skip writing and just return the tibble. Has no default: every caller states where the table goes.

Value

A tibble with one row per gene.