Config files handling

SINGE_Example.m

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+%% Simple example that runs SCINGE for two replicates of two hyperparameter settings
+clear all;
+close all;
+clc;
+if ~isdeployed
+    addpath(genpath('.'));
+end
+
+%% Import list of parameter combinations
+fid = fopen('SINGE_params.cfg');
+temp = fgetl(fid);
+while any(temp~=-1)||isempty(temp)
+    if ~isempty(temp)
+        temp = strsplit(temp);
+        pid = str2num(temp{1});
+        pname = temp{2};
+        pval = temp{3};
+        if isnumeric(str2num(pval))&&~isempty(str2num(pval))
+            pval = str2num(pval);
+        else
+            ind = find(pval=='''');
+            pval(ind) = [];
+        end
+        param_list{pid}.(pname) = pval;
+    end
+temp = fgetl(fid);
+end
+%% Specify Path to Input data and path to Output folder, gene_list and number of subsampled replicates
+fid = fopen('SINGE_IO.cfg');
+temp = fgetl(fid);
+while any(temp~=-1)||isempty(temp)
+    if ~isempty(temp)
+        temp = strsplit(temp);
+        pname = temp{1};
+        pval = temp{2};
+        if isnumeric(str2num(pval))&&~isempty(str2num(pval))
+            pval = str2num(pval);
+        else
+            ind = find(pval=='''');
+            pval(ind) = [];
+        end
+        IO.(pname) = pval;
+    end
+temp = fgetl(fid);
+end
+%% Run SINGE
+[ranked_edges, gene_influence] = SINGE(IO.gene_list,IO.Data,IO.outdir,IO.num_replicates,param_list);

SINGE_IO.cfg

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+Data data1/X_SCODE_data.mat
+outdir Output
+num_replicates 2
+gene_list data1/tf.mat

SINGE_config.cfg

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+1 ID   541
+1 lambda   0.01
+1 dT   10
+1 num_lags   5
+1 kernel_width   2
+1 prob_zero_removal   0
+1 prob_remove_samples   0.2
+1 family   'gaussian'
+1 date   '01/31/2019'
+
+2 ID   542
+2 lambda   0.01
+2 dT   5
+2 num_lags   9
+2 kernel_width   4
+2 prob_zero_removal   0.2
+2 prob_remove_samples   0.1
+2 family   'gaussian'
+2 date   '31-Jan-2019'

SINGE_params.cfg

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+1 ID   541
+1 lambda   0.01
+1 dT   10
+1 num_lags   5
+1 kernel_width   2
+1 prob_zero_removal   0
+1 prob_remove_samples   0.2
+1 family   'gaussian'
+1 date   '01/31/2019'
+
+2 ID   542
+2 lambda   0.01
+2 dT   5
+2 num_lags   9
+2 kernel_width   4
+2 prob_zero_removal   0.2
+2 prob_remove_samples   0.1
+2 family   'gaussian'
+2 date   '31-Jan-2019'

code/SINGE.m

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+function [ranked_edges, gene_influence] = SCINGE(gene_list,Data,outdir,num_replicates,param_list)
+% [ranked_edges, gene_influence] = SCINGE(gene_list,Data,outdir,num_replicates,param_list)
+% Standalone SCINGE implementation. 
+% Inputs:
+% gene_list = N x 1 cell array with list of relevant genes in the data set
+% Data = string representing the path of mat file containing the expression
+% data corresponding to above gene_list in the form of cell array X.
+% outdir = directory path to store individual GLG test results before Borda
+% aggregation
+% num_replicates = number of subsampled replicates (global SCINGE parameter)
+% param_list = list of hyperparameter combinations for individual GLG tests
+% Outputs:
+% ranked_edges = ranked list of gene interactions with corresponding SCINGE scores
+% gene_influence = ranked lists of regulators (genes) with corresponding SCINGE influence
+SINGE_version = '0.1.0';
+display(SINGE_version);
+for rep = 1:num_replicates
+    for ii = 1:length(param_list)
+        GLG_Instance(Data,'lambda',param_list{ii}.lambda,'dT',param_list{ii}.dT,'num_lags',param_list{ii}.num_lags,'kernel_width',param_list{ii}.kernel_width,'prob_zero_removal',param_list{ii}.prob_zero_removal,'replicate',rep,'ID',param_list{ii}.ID,'outdir',outdir,'family',param_list{ii}.family,'prob_remove_samples',param_list{ii}.prob_remove_samples,'date',param_list{ii}.date);
+    end
+end
+Str = Data;
+Str(Str=='.') = 'p';
+
+lind = max(max(strfind(Str,filesep)),0);
+mind = length(Str);
+if isempty(mind)||(mind<lind)
+    mind = length(Str);
+end
+Str = Str(lind+1:mind);
+Agg = Modified_Borda_Aggregation(Str,outdir);
+load(gene_list);
+ranked_edges = adjmatrix2edgelist(Agg,gene_list);
+[influence,ind] = sort(sum(Agg,2),'descend');
+gene_influence = [cell2table(gene_list(ind)) array2table(influence)];
+gene_influence.Properties.VariableNames{1} = 'Gene_Name';
+ranked_edgesw = ranked_edges;
+ranked_edgesw.SCINGE_Score = floor(ranked_edgesw.SCINGE_Score*10^5)/10^5;
+gene_influencew = gene_influence;
+gene_influencew.influence = floor(gene_influencew.influence*10^5)/10^5;
+writetable(ranked_edgesw,fullfile(outdir,'SCINGE_Ranked_Edge_List.txt'),'WriteVariableNames',true,'WriteRowNames',false,'Delimiter','\t');
+writetable(gene_influencew,fullfile(outdir,'SCINGE_Gene_Influence.txt'),'WriteVariableNames',true,'WriteRowNames',false,'Delimiter','\t');