SearchBM: SearchBM

In metaOmics/MetaDCN: Meta-analysis framework for differential coexpression network (DCN) detection

Description

Search for differentially co-expressed basic modules

Usage

SearchBM(GeneNetRes, MCSteps = 500, jaccardCutoff = 0.8, repeatTimes = 10,
  outputFigure = TRUE, silent = FALSE)

Arguments

GeneNetRes	a list from GeneNet function.
MCSteps	a number to specify the maximum number of MC steps for simulated annealing. Large number will be time-consuming.
jaccardCutoff	a number to specify the maximum jaccard index allowed between basic modules.
repeatTimes	a number to specify how many repeats of different seeds to be used. Large number will be time-consuming.
outputFigure	TRUE/FALSE to specify if figures are generated.
silent	TRUE/FALSE to specify if suppress screen output.

Details

This function will search for basic modules differentially co-expressed between case and control

Value

SearchBM will return a list and several Rdata, csv and png files saved in the folder path specified in GeneNet inputs.

List of basic module information:

w1	w1 weight with the most basic modules detected
BMInCase	data matrix listing the information of basic modules higher correlated in case
BMInControl	data matrix listing the information of basic modules higher correlated in control

permutation_energy_direction_p.Rdata is a list of energies of basic modules from permutation p.

basic_modules_summary_direction_weight_w.csv is a summary of basic modules detected using weight w in forward/backward search.

threshold_direction.csv is a table listing number of basic modules detected under different FDRs in forward/backward search.

figure_basic_module_c_repeat_r_direction_weight_w.png is a plot of basic module from component c repeat r using weight w in forward/backward search.

Author(s)

Li Zhu ([e-mail])

metaOmics/MetaDCN documentation built on May 29, 2019, 4:43 a.m.