Description Usage Arguments Value
This function determines the optimal values for the isolation parameter in the two step propagation, one value for the propagation with the gene-fragment network and one with the fragment-fragment network
1 | tuning_prop_vars(gf_net, ff_net, input_m, info = NULL, n_cores = 2)
|
gf_net |
Edge list of the chromatin interaction network such that first column are genes and second column are "FragX" fragments |
ff_net |
Edge list of the chromatin interaction network such that first and second column are "FragX" fragments |
input_m |
numeric matrix of cell profile, one column of a cell, rows are genes or fragments, values are expression or IAS |
info |
2-column dataframe, first column is character vector of node names, second colum is numeric vector of number of enhancer annotations associated to a node |
n_cores |
number of cores to run the function with parallel computing |
List of two elements: combinations and best_comb combinations contains all the pair of values tested best_comb contains only the optimal two values of the isolation paramter for the first and second overall propagation
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