updated gpl3 headers

R/RWR_CV.R

@@ -2,7 +2,20 @@
 # Perform K-fold Cross Validation on a gene set using RWR to find the RWR rank of the left-out genes
 # - Input: Pre-computed multiplex network and a geneset
 # - Output: Table with the ranking of each gene in the gene set when left out, along with AUPRC and AUROC curves
-# Author: David Kainer
+# Copyright (C) 2022  David Kainer
+# 
+# This file is part of RWRtoolkit.
+# 
+# RWRtoolkit is free software: you can redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the Free Software Foundation, either version 3
+# of the License, or (at your option) any later version.
+# 
+# RWRtoolkit is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; 
+# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License along with RWRtoolkit. 
+# If not, see <https://www.gnu.org/licenses/>.
 ########################################################################
 
 #' @importFrom dplyr %>%

R/RWR_LOE.R

@@ -3,11 +3,23 @@
 #    network or (2) ranking of genes in a provided second geneset.
 # - Input: Pre-computed multiplex network and at least one geneset of seeds.
 # - Output: Table with the ranking of genes from (1) network or (2) second geneset
-# Author: David Kainer
+# Copyright (C) 2022  David Kainer
+# 
+# This file is part of RWRtoolkit.
+# 
+# RWRtoolkit is free software: you can redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the Free Software Foundation, either version 3
+# of the License, or (at your option) any later version.
+# 
+# RWRtoolkit is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; 
+# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License along with RWRtoolkit. 
+# If not, see <https://www.gnu.org/licenses/>.
 ####################################################################################################
 
 #' @importFrom dplyr %>%
-
 ########################################################################
 # Internal Functions
 ########################################################################

R/RWR_make_multiplex.R

@@ -2,8 +2,20 @@
 # Generates a homogenous or heterogeneous multiplex network for downstream functions
 # - Input: A file list of a set of network
 # - Output: A multiplex object
-# Author: David Kainer
-####################################################################################################
+# Copyright (C) 2022  David Kainer
+# 
+# This file is part of RWRtoolkit.
+# 
+# RWRtoolkit is free software: you can redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the Free Software Foundation, either version 3
+# of the License, or (at your option) any later version.
+# 
+# RWRtoolkit is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; 
+# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License along with RWRtoolkit. 
+# If not, see <https://www.gnu.org/licenses/>.####################################################################################################
 
 #' @importFrom dplyr %>%
 #' @importFrom foreach %do%

R/RWR_netscore.R

@@ -2,8 +2,20 @@
 # Performs a network intersect between an input network and a gold truth network. It scores the strength of that intersect with multiple metrics.
 # - Input: A gold standard network as reference and another network to compare to the gold standard.
 # - Output: Table of metrics as a comparison between networks
-# Author: David Kainer
-########################################################################
+# Copyright (C) 2022  David Kainer
+# 
+# This file is part of RWRtoolkit.
+# 
+# RWRtoolkit is free software: you can redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the Free Software Foundation, either version 3
+# of the License, or (at your option) any later version.
+# 
+# RWRtoolkit is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; 
+# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License along with RWRtoolkit. 
+# If not, see <https://www.gnu.org/licenses/>.########################################################################
 
 
 ########################################################################

R/RWR_shortestpaths.R

@@ -4,8 +4,20 @@
 #   find the shortest paths for pairs of genes between gene sets.
 # - Input: Pre-computed multiplex network and one or two genesets
 # - Output: Edge list table
-# Author: David Kainer
-########################################################################
+# Copyright (C) 2022  David Kainer
+# 
+# This file is part of RWRtoolkit.
+# 
+# RWRtoolkit is free software: you can redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the Free Software Foundation, either version 3
+# of the License, or (at your option) any later version.
+# 
+# RWRtoolkit is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; 
+# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License along with RWRtoolkit. 
+# If not, see <https://www.gnu.org/licenses/>.########################################################################
 
 #' @importFrom dplyr %>%
 #' @importFrom foreach %dopar%

R/utils.R

@@ -1,6 +1,21 @@
 ########################################################################
 # Common functions for RWRtoolkit.
 ########################################################################
+# Copyright (C) 2022  David Kainer
+# 
+# This file is part of RWRtoolkit.
+# 
+# RWRtoolkit is free software: you can redistribute it and/or modify it under the terms of the 
+# GNU General Public License as published by the Free Software Foundation, either version 3
+# of the License, or (at your option) any later version.
+# 
+# RWRtoolkit is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; 
+# without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+# See the GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License along with RWRtoolkit. 
+# If not, see <https://www.gnu.org/licenses/>.
+########################################################################
 
 load_geneset = function(path, nw.mpo=NULL, verbose=FALSE) {
     if (is.null(path)) {