compute.spec.single: This is to calculate the similarity between: 1. the label...

In gsdensity: Density-Based Gene Set Specificity Evaluation

This is to calculate the similarity between: 1. the label propagation probability of cells for gene sets and 2. the identify of cells in a certain partition This is called by 'compute.spec'; can also run by itself

Description

This is to calculate the similarity between: 1. the label propagation probability of cells for gene sets and 2. the identify of cells in a certain partition This is called by 'compute.spec'; can also run by itself

Usage

## S3 method for class 'spec.single'
compute(vec, positive, cell_df)

Arguments

vec	cell partition vector (usually a column name in [e-mail])
positive	the positive label, e.g. "disease" or "cluster_1"
cell_df	the output of run.rwr.list

Value

specificity of a pathway activity and other levels of cell annotations (e.g., cell type)

gsdensity documentation built on March 31, 2023, 8:32 p.m.