ref_sim_spectrum: Calculate Reference Similarity Spectrum

In quadbiolab/simspec: Calculate data representation of Reference/Cluster Similarity Spectrum

Calculate Reference Similarity Spectrum

Description

Calculate Reference Similarity Spectrum (RSS), given expression of the data and expression of the external reference data set.

Usage

ref_sim_spectrum(object, ...)

## Default S3 method:
ref_sim_spectrum(
  object,
  ref,
  method = c("pearson", "spearman"),
  use_fast_rank = TRUE,
  scale = TRUE
)

## S3 method for class 'Seurat'
ref_sim_spectrum(
  object,
  ref,
  as_assay = FALSE,
  assay.name = "RSS",
  reduction.name = "rss",
  reduction.key = "RSS_",
  ...
)

Arguments

object	An object
ref	Expression matrix of the reference data set
method	Correlation method
use_fast_rank	When the presto package is available, use its rank_matrix function to rank sparse matrix
scale	If TRUE, z-transform is applied to the calculated similarities across reference samples
as_assay	When it is TRUE, the output is returned as an Assay object in the Seurat object
assay.name	Assay name of the RSS representation in the returned Seurat object
reduction.name	Reduction name of the RSS representation in the returned Seurat object
reduction.key	Reduction key of the RSS representation in the returned Seurat object

quadbiolab/simspec documentation built on March 8, 2024, 11:59 p.m.