do_reciprocal_neighbor_graph: Construct a graph based on selected genes in a ClusterSet...

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Construct a graph based on selected genes in a ClusterSet object and their neighbors

Description

This function creates a graph based on the gene selected by select_genes() and their neighbors. It generates an input file required for the MCL (Markov Cluster) algorithm.

Usage

do_reciprocal_neighbor_graph(object = NULL, output_path = NULL, name = NULL)

Arguments

object	A ClusterSet object.
output_path	a character indicating the path where the output files will be stored.
name	a character string giving the name for the output files. If NULL, a random name is generated.

Value

The output of this function is a tab-separated file, which serves as input for the MCL algorithm.

Examples

# Set verbosity to 1 to display info messages only.
set_verbosity(1)

# Create a matrix with 4 signatures
m <- create_4_rnd_clust()

# Select informative features
res <- select_genes(m[1:600,],
                    distance = "pearson",
                    k = 75,
                    noise_level = 0.3,
                    fdr = 1e-8,
                    row_sum = -Inf)
                    
# Construct a graph based on genes selected with select_genes() and their neighbors
do_reciprocal_neighbor_graph(object = res)

dputhier/scigenex documentation built on Dec. 20, 2024, 2:22 a.m.