Compute mutual rank from a similarity matrix

Computes the mutual rank (MR) for all pairs in a symmetric similarity or dissimilarity matrix, a robust measure frequently used to stabilize pairwise similarity relationships.

Usage

mutual.rank(mat, num_threads = -1)

Arguments

mat

Numeric symmetric matrix (dense or sparse) representing pairwise similarities or dissimilarities.

num_threads

Integer; number of threads to use. Default -1 uses all available cores.

Value

A numeric matrix of mutual ranks with the same dimensions as mat.

See also

jaccard.sparse, markoClust

Examples

utils::data("pbmc_small", package = "SeuratObject")

mat <- SeuratObject::LayerData(
  pbmc_small,
  assay = "RNA",
  layer = "counts"
)

binary_mat <- sign(mat)

similarity_matrix <- jaccard.sparse(
  binary_mat,
  num_threads = 1
)

mr <- mutual.rank(
  similarity_matrix,
  num_threads = 1
)