get_wgcna: Utilize WGCNA function

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Utilize WGCNA function

Description

Run the WGCNA package on the processed data.

Usage

get_wgcna(data, n_genes, soft_power, min_module_size)

Arguments

data	Data matrix that has been through the pre-processing
n_genes	Number of most variable genes to use in the function
soft_power	Value between 1-20 (https://support.bioconductor.org/p/87024/)
min_module_size	For modules detected by WGCNA, set a minimum size

Value

A list of 8 objects. data is a submatrix of the input parameter data which on contains the genes that were selected with n_genes. powers is a numeric vector from 1-10 and then the even numbers from 10-20. sft is a return from the WGCNA package that is a list containing powerEstimate and fitIndices. For information on these objects visit https://www.rdocumentation.org/packages/WGCNA/versions/1.70-3/topics/pickSoftThreshold. tom is another return from the WGCNA package, for information on this matrix visit https://www.rdocumentation.org/packages/WGCNA/versions/1.70-3/topics/TOMsimilarityFromExpr. dynamic_colors is a vector of colors created by the WGCNA package to correspond to the modules that were identified by the pacakage. module_info is a data frame with a gene name, a color, and the identified module for the gene. n_modules gives the number of modules calculated. n_genes tells the number of genes included in the modules.

espors/idepGolem documentation built on April 23, 2024, 1:11 p.m.