FindParaModule: Find suitable parameters for partitioning pathways modules
In BioM2: Biologically Explainable Machine Learning Framework

FindParaModule

R Documentation

Find suitable parameters for partitioning pathways modules

Description

Find suitable parameters for partitioning pathways modules

Usage

FindParaModule(
  pathways_matrix = NULL,
  control_label = 0,
  minModuleSize = seq(10, 20, 5),
  mergeCutHeight = seq(0, 0.3, 0.1),
  minModuleNum = 5,
  power = NULL,
  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 )
`minModuleSize`	minimum module size for module detection. Detail for WGCNA::blockwiseModules()
`mergeCutHeight`	dendrogram cut height for module merging. Detail for WGCNA::blockwiseModules()
`minModuleNum`	Minimum total number of modules detected
`power`	soft-thresholding power for network construction. Detail for WGCNA::blockwiseModules()
`exact`	Whether to divide GO pathways more accurately (work when ancestor_anno=NULL)
`ancestor_anno`	Annotations for ancestral relationships (like data('GO_Ancestor') )