Update the correlation matrix to a TOM

This function will update the correlation matrix to a topological overlap matrix. It defaults to "v2" and the signed version, please see calculate_tom() for details.

Usage

cor_module_tom(object, signed = TRUE, version = c("v2", "v1"), .verbose = TRUE)

Arguments

object

The class, see BulkCoExp(). You need to have applied cor_module_processing() before applying this function.

signed

Boolean. Do you want to use the signed or unsigned version. Defaults to TRUE.

version

String. One of c("v2", "v1"). Defaults to "v2".

.verbose

Boolean. Controls verbosity of the function.

Value

The class with added data to the properties for subsequent usage.

Examples

# replace the stored correlations with a signed topological overlap
mat <- t(synthetic_signal_matrix()$mat)
obj <- BulkCoExp(mat, data.table::data.table(sample_id = rownames(mat)))
obj <- preprocess_bulk_coexp(obj, hvg = 0.3, .verbose = FALSE)
obj <- cor_module_processing(obj, cor_method = "spearman", .verbose = FALSE)
obj <- cor_module_tom(obj, signed = TRUE, version = "v2", .verbose = FALSE)
obj@params$correlation_params$TOM
#> [1] TRUE