R/util_graph.R

In cbg-ethz/knockdown: Statistical Analysis of High-Throughput Genetic Perturbation Screens

# perturbatr: analysis of high-throughput gene perturbation screens
#
# Copyright (C) 2018 Simon Dirmeier
#
# This file is part of perturbatr
#
# perturbatr 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.
#
# perturbatr 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 perturbatr. If not, see <http://www.gnu.org/licenses/>.


#' @noRd
#' @importFrom igraph graph_from_data_frame
read.graph <- function(graph)
{
  if (!base::is.data.frame(graph))
    stop("graph needs to be a data.frame/tibble")
  if (! "weight" %in% colnames(graph))
    stop("graph needs a column named weight")
  if (!is.numeric(graph$weight))
    stop("graph$weight needs to be numeric")

  gra <- igraph::graph_from_data_frame(graph, directed=FALSE)
  gra
}