add_counts: Add counts to vesalius assay Adding custom count matrix to a...

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

Add counts to vesalius assay Adding custom count matrix to a vesalius assay object.

Description

Add counts to vesalius assay Adding custom count matrix to a vesalius assay object.

Usage

add_counts(
  vesalius_assay,
  counts,
  raw_counts = NULL,
  add_name = NULL,
  force = FALSE,
  verbose = TRUE
)

Arguments

vesalius_assay	a vesalius assay object
counts	matrix or sparse matrix containing normalised counts
raw_counts	matrix or sparse matrix containing raw counts
add_name	character string defining the name of the count matrix being added.
force	logical indicating if count matrix provided should also be used as raw count matrix.
verbose	logical indicating if progress messages should be outputed.

Details

In some case, you might wish to use your own normalisation method. In this case, you can add your own matrix and specify the name you want to give to that count matrix.

Differential gene expression tools such as DESeq2 and edgeR require raw counts. As such, we recommend providing raw counts as well. If you do not have raw counts, or do not wish to provide them, you can set the force argument to TRUE. This will force vesalius to generate a copy of your count matrix and use this as "raw" count matrix.

Since coordinates need to be parsed to the vesalius_assay contructor, this function will also compared the your count matrix to the coordinate data. It will trim the count matrix based on barcodes shared between both.

Value

a vesalius_assay object

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.