Merge branch 'development'

Conflicts:
	DESCRIPTION
	README.md
	vignettes/vignette.Rnw

.Rbuildignore

@@ -0,0 +1,3 @@
+^README.md$
+^.gitignore$
+^.git/.*$

.gitignore

@@ -1,13 +1,27 @@
-# History #
-###########
-.history
-
-# OS generated files #
-######################
-.DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
+/cfg.R
+# History files
+.Rhistory
+.Rapp
+*.history
+
+# Example code in package build process
+*-Ex.R
+
+# RStudio files
+*.RData
+.Rproj.user/
+.Rproj
+.Rproj.user
+*.Rdata
+*.Rproj
+
+# TRONCO Output
+*.pdf
+*.tar.gz
+*.tex
+*.mat
+*.zip
+*.png
+
+# Configuration file
+cfg.R

DESCRIPTION

@@ -1,47 +1,60 @@
 Package: TRONCO
-Version: 1.1.0
-Date: 2014-09-22
+Version: 2.0.0-8
+Date: 2015-07-21
 Title: TRONCO, a  package for TRanslational ONCOlogy
-Author: Marco Antoniotti, Giulio Caravagna,
-    Alex Graudenzi, Ilya Korsunsky,
-    Mattia Longoni, Loes Olde Loohuis,
-    Giancarlo Mauri, Bud Mishra, Daniele Ramazzotti
-Maintainer: Giulio Caravagna <[email protected]>,
-    Alex Graudenzi <[email protected]>,
-    Daniele Ramazzotti <[email protected]>
-Depends:
-    R (>= 2.10),
-    methods,
+Authors@R: 
+    c(person("Marco", "Antoniotti", role=c("cph")), 
+    person("Giulio", "Caravagna", role=c("aut", "cre"), email="[email protected]"),
+    person("Luca", "De Sano", role=c("aut"), email="[email protected]"), 
+    person("Alex", "Graudenzi", role=c("aut"), email="[email protected]"), 
+    person("Ilya", "Korsunsky", role=c("cph")),
+    person("Mattia", "Longoni", role=c("ctb")), 
+    person("Loes", "Olde Loohuis", role=c("cph")),
+    person("Giancarlo", "Mauri", role=c("cph")), 
+    person("Bud", "Mishra", role=c("cph")), 
+    person("Daniele", "Ramazzotti", role=c("aut"), email="[email protected]"))
+Depends: 
+    R (>= 3.1),
+    doParallel,
+    bnlearn,
+Imports:
     Rgraphviz,
-    lattice,
-    graph
-Description: Genotype-level cancer progression models describe the ordering of
-    accumulating mutations, e.g., somatic mutations / copy number variations,
-    during cancer development. These graphical models help understand the
-    causal structure involving events promoting cancer progression, possibly
-    predicting complex patterns characterising genomic progression of a cancer.
-    Reconstructed models can be used to better characterise genotype-phenotype
-    relation, and suggest novel targets for therapy design. TRONCO
-    (TRanslational ONCOlogy) is a R package aimed at collecting
-    state-of-the-art algorithms to infer progression models from
-    cross-sectional data, i.e., data collected from independent patients which
-    does not necessarily incorporate any evident temporal information. These
-    algorithms require a binary input matrix where: (i) each row represents a
-    patient genome, (ii) each column an event relevant to the progression (a
-    priori selected) and a 0/1 value models the absence/presence of a certain
-    mutation in a certain patient. The current first version of TRONCO
-    implements the CAPRESE algorithm (Cancer PRogression Extraction with Single
-    Edges) to infer possible progression models arranged as trees; cfr.
-    Inferring tree causal models of cancer progression with probability
-    raising, L. Olde Loohuis, G. Caravagna, A. Graudenzi, D. Ramazzotti, G.
-    Mauri, M. Antoniotti and B. Mishra. PLoS One, to appear. This vignette
-    shows how to use TRONCO to infer a tree model of ovarian cancer progression
-    from CGH data of copy number alterations (classified as gains or losses
-    over chromosome's arms). The dataset used is available in the SKY/M-FISH
-    database.
-License: EPL (>= 1.0)
+    ggplot2,
+    RColorBrewer,
+    reshape2,
+    cgdsr,
+    igraph,
+    grid,
+    gridExtra,
+    xtable,
+    gtable,
+    scales
+Suggests: 
+    BiocGenerics,
+    BiocStyle,
+    testthat,
+    R.matlab
+Description: 
+    TRONCO (TRanslational ONCOlogy) is a R package which collects 
+    algorithms to infer progression models from Bernoulli 0/1 profiles of genomic
+    alterations across a tumor sample. Such profiles are usually visualised as a 
+    binary input matrix where each row represents a patient's sample (e.g., the 
+    result of a sequenced tumor biopsy), and each column an event relevant to the 
+    progression (a certain type of somatic mutation, a focal or higher-level 
+    chromosomal copy number alteration etc.); a 0/1 value models the absence/presence
+    of that alteration in the sample. In this version of TRONCO such profiles can 
+    be readily imported by boolean matrices and MAF/GISTIC files. The package provides
+    various functions to editing, visualise and subset such data, as well as functions 
+    to query the Cbio portal for cancer genomics. This version of TRONCO comes with
+    the parallel implementations the CAPRESE  [PLoS ONE 9(12): e115570] and CAPRI 
+    [Bioinformatics, doi:10.1093/bioinformatics/btv296] algorithms to infer possible
+    progression models arranged as trees, or general direct acyclic graphs. 
+    Bootstrap functions to assess the parametric, non-prametric and statistical 
+    confidence of every inferred model are also provided. The package comes with 
+    some data available as well, which include the dataset of Atypical Chronic Myeloid 
+    Leukemia samples provided by Piazza et al., Nat. Genet., 45 (2013), and examples.
+LazyData: TRUE
+License: GPL (>= 3.0)
 URL: http://bimib.disco.unimib.it
+BugReports: https://github.com/BIMIB-DISCo/TRONCO
 biocViews: Cancer
-Suggests:
-    RUnit,
-    BiocGenerics