thresholdWGCNAmodules: Remove genes from modules if connectivity is below a...

In mjdufort/WGCNAtools: Simplify use of WGCNA

Remove genes from modules if connectivity is below a specified threshold

Description

Remove genes from WGCNA modules if connectivity to the module (kME) is below a specified threshold. All such genes are assigned to a new module, which can be named by the user.

Usage

thresholdWGCNAmodules(gene_modules, threshold = 0.25, color.no_mod = "white",
  color_col = "color_assigned", kME_col = "kME_color_assigned")

Arguments

gene_modules	A data frame genes, with columns for the assigned module and connectivity to module.
threshold	The connectivity threshold; genes with connectivity below this value will be removed. Defaults to 0.25.
color.no_mod	The name for the new module, to which genes not meeting the threshold will be assigned.
color_col	Optional, the name or number of the column in gene_modules which contains the module names.
kME_col	Optional, the name or number of the column in gene_modules which contains the connectivity values.

Value

A new data frame with the same dimension and names as gene_modules, with 0 or more genes assigned to the new module.

mjdufort/WGCNAtools documentation built on Oct. 10, 2024, 12:25 p.m.