R/easyLook.R

In clipper: Gene Set Analysis Exploiting Pathway Topology

# Copyright 2012 Paolo Martini <paolo.martini@unipd.it>
#
#
# This file is part of clipper.
#
# clipper is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License
# version 3 as published by the Free Software Foundation.
#
# clipper 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public
# License along with clipper. If not, see <http://www.gnu.org/licenses/>.


easyLook <- function (clipped) {
  if (is.null(clipped))
    return(NULL)
  for (i in 1:NROW(clipped)) {
    genes <- unique(unlist(strsplit(clipped[i,"involvedGenes"],";")))
    clipped[i,"involvedGenes"] <- paste(genes, collapse=";")
  }
  clipped[,c("maxScore", "involvedGenes")]
}