PathwaysModule {BioM2}

Delineate differential pathway modules with high biological interpretability

Description

Delineate differential pathway modules with high biological interpretability

Usage

PathwaysModule(
  pathways_matrix = NULL,
  control_label = NULL,
  power = NULL,
  minModuleSize = NULL,
  mergeCutHeight = NULL,
  cutoff = 70,
  MinNumPathways = 5,
  p.adjust.method = "fdr",
  exact = TRUE,
  ancestor_anno = NULL
)

Arguments

pathways_matrix

A pathway matrix generated by the BioM2( target='pathways') function.

control_label

The label of the control group ( A single number, factor, or character )

power

soft-thresholding power for network construction. Detail for WGCNA::blockwiseModules()

minModuleSize

minimum module size for module detection. Detail for WGCNA::blockwiseModules()

mergeCutHeight

dendrogram cut height for module merging. Detail for WGCNA::blockwiseModules()

cutoff

Thresholds for Biological Interpretability Difference Modules

MinNumPathways

Minimum number of pathways included in the biologically interpretable difference module

p.adjust.method

p-value adjustment method.(holm", "hochberg", "hommel", "bonferroni", "BH", "BY",

exact

Whether to divide GO pathways more accurately (work when ancestor_anno=NULL)

ancestor_anno

Annotations for ancestral relationships (like data('GO_Ancestor') )

Value

A list containing differential module results that are highly biologically interpretable