def_net_module2: Identify the the edge of the modules (blocks) within the net...

In naikai/sake: Single-cell RNA-Seq Analysis and Klustering Evaluation

Identify the the edge of the modules (blocks) within the net connectivity matrix

Description

Run for loops to detect the block Detect edge genes in each block and their gene idx Go back to the original 100x100 matrix and use the edge genes (idx) to define block

Usage

def_net_module2(core_sub_jaccard_dist, sub_jaccard_dist,
  min.connectivity = 0.2, min.size = 5, start_idx = 1,
  allow.gap = 1)

Arguments

core_sub_jaccard_dist	preprocessed sub_jaccard_dist matrix (after applying filter, binarized the data)
sub_jaccard_dist	zoomed-in small block size of jaccard_dist
min.connectivity	threshold for minimum connectivity (set to 75% quartile in each block)
min.size	threshold for minimum block size
start_idx	specifiy what is the index for the starting gene in the block
allow.gap	allow how man gaps between each sub-modules

Examples

def_net_modules2(core_sub_jaccard_dist, sub_jaccard_dist, min.connectivity=0.2, min.size=5)

naikai/sake documentation built on Feb. 15, 2023, 11 p.m.