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