get_cor: Extract correlation matrix

In bschilder/scKirby: Automated ingestion and conversion of various single-cell data formats.

Extract correlation matrix

Description

Extract correlation matrix stored as a graph.

Usage

get_cor(
  obj,
  keys = NULL,
  assay = NULL,
  slot = NULL,
  graph_key = NULL,
  method = "pearson",
  return_obj = FALSE,
  as_graph = TRUE,
  verbose = TRUE
)

Arguments

obj	A single-cell object supported by scKirby. See converters for a table of all supported conversions.
keys	The keys of reductions to extract from.
assay	Assay to used to compute correlation graph if one does not already exist.
slot	Name of component object to return
graph_key	Name of the graph to extract.
method	Pairwise correlation method.
return_obj	Whether to return the single-cell object with a new graph, or to simply return the sparse correlation matrix.
as_graph	Convert the correlation matrix to the Graphs class.
verbose	Print messages.

Value

Trait-trait correlation matrix.

Examples

obj <- example_obj("seurat")
Xcor <- get_cor(obj = obj,
                keys = "pca")

bschilder/scKirby documentation built on April 22, 2024, 12:13 a.m.