integrate_counts: Integrate counts using Seurat

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

Integrate counts using Seurat

Description

Integrate counts using Seurat

Usage

integrate_counts(
  matched,
  reference,
  method = "HarmonyIntegration",
  nfeatures = 2000,
  dimensions = 30,
  infer = FALSE,
  signal = "variable_features",
  verbose
)

Arguments

matched	matrix - matrix containing counts from matched/mapped assay
reference	matrix - matrix containing counts from reference assay
method	character - Seurat integration method to use
nfeatures	integer - number of features to use during integration
dimensions	interger - number of dimensions integrated latent space dimensions.
infer	logical - back infer original counts by reversing reduced dimensional space roations.
signal	character - defining which signal should be returned: variable_features, all_features or custom gene list.
verbose	logical - print output messages

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