Description Usage Arguments Details Value Author(s)
Search for differentially co-expressed basic modules
1 2 |
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. |
This function will search for basic modules differentially co-expressed between case and control
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.
Li Zhu (liz86@pitt.edu)
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