comparePhenotypes: Obtain the Module Information from Consensus-Based...

In zhouLabNCSU/C3NA: Correlation and Consensus-Based Cross-Taxonomy Network Analysis (C3NA)

Obtain the Module Information from Consensus-Based Investigation

Description

Extract the module information based on the consensus results.

Usage

comparePhenotypes(
  C3NAObj_Comparison = C3NAObj1,
  C3NAObj_Reference = C3NAObj2,
  corCutoff = 0.2,
  fdr = 0.05,
  unusefulTaxa = NA,
  verbose = 0,
  nBootstrap = 300
)

Arguments

C3NAObj_Comparison	(Required) The C3NAObj with a single phenotype as Disease.
C3NAObj_Reference	(Required) The C3NAObj with a single phenotype as Control.
corCutoff	(Required) A positive correlation cut-off point, default is 0.2.
fdr	(Required) BH-Adjusted p-value, default is 0.05.
unusefulTaxa	(Optional) A list of taxa names that could not be interpreated biologically, e.g. human_gut, ambiguous_taxa
verbose	(Optinal) Verbose for the module preservation analysis, the higher the more detailed output.
nBootstrap	(Optional) Number of bootstrap for the module preservation.

zhouLabNCSU/C3NA documentation built on Oct. 10, 2022, 4:43 a.m.