construct_pseudocells: Construct pseudocells by averaging transcriptome of similar...

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

Construct pseudocells by averaging transcriptome of similar cells

Description

This function implements the procedure to average the expression profiles of similar cells in order to construct pseudocells

Usage

construct_pseudocells(
  knn_adj,
  ratio,
  init_dist = 1,
  max_dist = 2,
  min_pooled_cells = 2,
  min_seed_num = 1,
  seed = 12345
)

Arguments

knn_adj	The adjacent matrix of the kNN network
ratio	The downsample rate
init_dist	Maximal distance on the kNN network to group a cell to the selected capital or pseudocell center
max_dist	A cell which is not grouped to any pseudocell territory is grouped to the closest one if its distance to the capital is no more than max_dist
min_pooled_cells	Only pseudocells covering at least this number of cells are valid
min_seed_num	The minimum number of seed capitals to start the procedure
seed	The base seed for randomly assigning a cell to a capital candidate

Value

A data.frame indicating indices of cells and pseudocells

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