FindParaModule {BioM2}

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') )

Value

A list containing recommended parameters