run_CoExpression: Preprocess the connecitivty matrix based on mean connectivity...

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

Preprocess the connecitivty matrix based on mean connectivity and binary switch 1. First try to remove columns (rows) that have median expression 75 2. Convert the matrix into binary based on quantile connectivity'

Description

Preprocess the connecitivty matrix based on mean connectivity and binary switch 1. First try to remove columns (rows) that have median expression 75 2. Convert the matrix into binary based on quantile connectivity'

Usage

run_CoExpression(expdata, thresh = "soft", tao = 0.7, beta = 10,
  method = "Pearson", folderName0 = "Module",
  avg_con_thresh = 0.00015, save.data = F)

Arguments

tao	threshold for hard transformation
beta	parameter for soft power transformation
data	Input expression data
num_features	Number of top high connective genes to be used

Examples

run_CoExpression(expdata)

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