Merge branch 'master' of github.com:antagomir/netresponse

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: netresponse
 Type: Package
-Title: netresponse: functional network analysis
-Version: 1.17.13
-Date: 2014-11-05
+Title: Functional Network Analysis
+Version: 1.19.0
+Date: 2015-03-24
 Author: Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen
 Maintainer: Leo Lahti <[email protected]>
 Description: Algorithms for functional network analysis. Includes an
@@ -21,14 +21,12 @@ Imports:
     ggplot2,
     graph,
     igraph,
-    methods,
     parallel,
     plyr,
     qvalue,
     RColorBrewer
 URL: https://github.com/antagomir/netresponse
 BugReports: https://github.com/antagomir/netresponse/issues
-LazyLoad: yes
 biocViews: CellBiology, Clustering, GeneExpression, Genetics, Network,
     GraphAndNetwork, DifferentialExpression, Microarray,
     Transcription

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.2): do not edit by hand
+# Generated by roxygen2 (4.1.0): do not edit by hand
 
 export(ICMg.combined.sampler)
 export(ICMg.get.comp.memberships)

R/NetResponseModel-accessors.R

@@ -225,7 +225,7 @@ setMethod("getqofz", "NetResponseModel", function (model, subnet.id, log = FALSE
 #' @examples
 #' ## Load a pre-calculated netresponse model obtained with 
 #' # model <- detect.responses(toydata$emat, toydata$netw, verbose = FALSE)
-#' # data( toydata ); get.subnets(toydata$model) 
+#' # data( toydata ); get.dat(toydata$model) 
 setMethod("get.dat", "NetResponseModel", function (model, subnet.id, sample = NULL) {
 
   # usage get.dat(model, subnet.id, sample = NULL)

R/firstlib.R

@@ -3,14 +3,14 @@
 #' @import parallel
 #' @import RColorBrewer
 #' @import Rgraphviz
-#' @import methods
 #' @importFrom igraph igraph.to.graphNEL
 #' @importFrom igraph igraph.from.graphNEL
 #' @importFrom igraph subgraph
 #' @importFrom igraph graph.data.frame
 #' @importFrom igraph graph.edgelist
 #' @import qvalue
 #' @import mclust
+#' @import methods
 #' @importFrom plyr ddply
 #' @importFrom minet build.mim
 #' @importFrom reshape melt
@@ -34,5 +34,5 @@
 
 .onAttach <- function(lib, pkg)
 {
-   packageStartupMessage('\nnetresponse Copyright (C) 2008-2014 Leo Lahti et al..\nThis program comes with ABSOLUTELY NO WARRANTY.\nThis is free software, and you are welcome to redistribute it under GNU GPL >=2, see the licensing terms for details.\n')
+   packageStartupMessage('\nnetresponse (C) 2008-2015 Leo Lahti et al.\n\nhttps://github.com/antagomir/netresponse')
 }

R/order.responses.R

@@ -1,16 +1,3 @@
-# Copyright (C) 2010-2013 Leo Lahti
-# Contact: Leo Lahti <[email protected]>
-#
-# This program 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 2, or (at your option)
-# any later version.
-#
-# This program 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.
-
 # Fixme: finish this later
 #order.samples <- function (subnet.id, model, phenodata, which.factor, response, method = "hypergeometric") {
 #    
@@ -51,19 +38,26 @@
 #'
 #' @return A data frame with elements 'ordered.responses' which gives a data
 #'   frame of responses ordered by enrichment score for the investigated sample.
-#'   The subnetwork, response id and enrichment score are shown. The method field
-#'   indicates the enrichment calculation method. The sample field lists the
-#'   samples et for which the enrichments were calculated. The info field lists
-#'   additional information on enrichment statistics.
+#'   The subnetwork, response id and enrichment score are shown. 
+#'   The method field indicates the enrichment calculation method. 
+#'   The sample field lists the samples et for which the enrichments 
+#'   were calculated. 
+#'   The info field lists additional information on enrichment statistics.
 #' @note Tools for analyzing end results of the model.
 #' @author Leo Lahti \email{leo.lahti@@iki.fi}
 #' @references See citation("netresponse") for citation details.
 #' @keywords utilities
 #' @export
 #' @examples #
-#' # - for given sample/s (factor level), order responses (across all subnets) by association strength (enrichment score)
-#' #order.responses(model, sample, method  = "hypergeometric") # overrepresentation
-order.responses <- function (models, sample, method = "hypergeometric", min.size = 2, max.size = Inf, min.responses = 2, subnet.ids = NULL, verbose = FALSE, data = NULL) {
+#' # - for given sample/s (factor level), 
+#' #     order responses (across all subnets) by association strength 
+#' #     (enrichment score); overrepresentation
+#' # order.responses(model, sample, method  = "hypergeometric") 
+order.responses <- function (models, sample, method = "hypergeometric", 
+		   	     min.size = 2, max.size = Inf, 
+			     min.responses = 2, 
+			     subnet.ids = NULL, 
+			     verbose = FALSE, data = NULL) {
 
     # Given sample (for instance set of samples associated with a given factor 
     # level) order the responses across all subnetworks based on their 
@@ -89,28 +83,22 @@ order.responses <- function (models, sample, method = "hypergeometric", min.size
 }
 
 
-
-
 #' List responses with significant associations to a given sample group.
 #' 
-#' List responses with significant associations to a given sample group.
-#' 
-#' 
 #' @param model NetResponseModel object.
 #' @param sample User-specified samples group for which the enrichments are
 #' calculated. For instance, an annotation category.
 #' @param qth q-value threshold for enrichments
 #' @param method Enrichment method.
-#' @return Table containing statistics of the significantly associated
-#' responses.
+#' @return Statistics of the significantly associated responses.
 #' @author Leo Lahti \email{leo.lahti@@iki.fi}
 #' @seealso response.enrichment
 #' @references See citation("netresponse")
 #' @keywords utilities
 #' @export
-#' @examples #
-#' 
-list.significant.responses <- function (model, sample, qth = 1, method = "hypergeometric") {
+#' @examples # 
+list.significant.responses <- function (model, sample, qth = 1, 
+			                method = "hypergeometric") {
 
   # Order responses according to their association with the given sample group
   o <- order.responses(model, sample = sample, method = "hypergeometric")$ordered.responses