1. OncoSimulR
  2. man
  3. simOGraph.Rd
Browse code

2.17.7: no longer depends on nem; more models from MAGELLAN

ramon diaz-uriarte (at Phelsuma) authored on 30/01/2020 13:39:14
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man/simOGraph.Rd
History View file @ eb53711
... ... 
@@ -84,7 +84,10 @@ sh. See \code{\link{allFitnessEffects}}}
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   input, as "restriction table" in  \code{\link{allFitnessEffects}}.
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 }
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-\author{Ramon Diaz-Uriarte}
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+\author{Ramon Diaz-Uriarte. Code for transitive closure taken from the
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+  nem package, whose authors are Holger Froehlich, Florian Markowetz,
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+  Achim Tresch, Theresa Niederberger, Christian Bender, Matthias Maneck,
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+  Claudio Lottaz, Tim Beissbarth}
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 \examples{
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 (a1 <- simOGraph(10))
Browse code

version 2.7.2 Changes in version 2.7.2 (2017-09-27): - genot_to_adj_mat in C++. - fast_peaks (for no backmutation cases). - Better explanation and testing of peaks and valleys. - Clarified simOGraph transitive reduction. - Better handling of ti corner cases. - Magellan reading fuctions adapted to output of newer (as of 2017-07) version of Magellan. - sorting gene names in allGenotypes_to_matrix. - sampledGenotypes: genotype names with sorted gene names.

ramon diaz-uriarte (at Phelsuma) authored on 27/09/2017 10:23:50
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man/simOGraph.Rd
History View file @ f9a38e2
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@@ -34,8 +34,9 @@ s = 0.1, sh = -0.1, typeDep = "AND")
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   \item{removeDirectIndirect}{
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     Ensure that no two nodes are connected both directly (i.e., with an
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   edge between them) and indirectly, through intermediate nodes. If
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-  TRUE, the direct connections are removed from the graph starting from
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-  the bottom.
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+  TRUE, we return the transitive reduction of the DAG.
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+  %% the final DAG returned is the transitive reduction of thethe direct
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+  %% connections are removed from the graph starting from the bottom.
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 }
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 \item{rootName}{
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   The name you want to give the "Root" node.
Browse code

v.2.5.2 - Lots and lots of addition to vignette including benchmarks. - Diversity of sampled genotypes. - Genotyping error can be added in samplePop. - LOD and POM (lines of descent, path of maximum, sensu Szendro et al.). - simOGraph can also out rT data frames. - Better (and better explained) estimates of simulation error for McFL.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@124982 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 10/12/2016 16:05:05
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man/simOGraph.Rd
History View file @ fc38a87
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@@ -7,8 +7,11 @@
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   Simulate DAGs that represent restrictions in the accumulation of mutations.
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 }
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 \usage{
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-simOGraph(n, h = 4, conjunction = TRUE, nparents = 3,
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-multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root")
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+simOGraph(n, h = ifelse(n >= 4, 4, n), conjunction = TRUE, nparents = 3,
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+multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root",
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+geneNames = seq.int(n), out = c("adjmat", "rT"),
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+s = 0.1, sh = -0.1, typeDep = "AND")
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+
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 }
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 \arguments{
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@@ -36,9 +39,27 @@ multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root")
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 }
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 \item{rootName}{
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   The name you want to give the "Root" node.
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+}
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+\item{geneNames}{
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+  The names you want to give the the non-root nodes.
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 }
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+
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+
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+\item{out}{Whether the ouptut should be an adjacency matrix  or a
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+  "restriction table", as used in   \code{\link{allFitnessEffects}}.}
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+
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+\item{s}{If using as output a restriction, the default value for s. See
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+\code{\link{allFitnessEffects}}.}
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+
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+\item{sh}{If using as output a restriction, the default value for
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+sh. See \code{\link{allFitnessEffects}}}
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+
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+\item{typeDep}{If using as output a restriction, the default value for
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+"typeDep". See \code{\link{allFitnessEffects}}}
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+
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 }
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+
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 \details{
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   This is a simple, heuristic procedure for generating graphs of
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   restrictions that seem compatible with published trees in the
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@@ -58,7 +79,9 @@ multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root")
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 }
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 \value{
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-  An adjacency matrix for a directed graph.
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+  An adjacency matrix for a directed graph or a data frame to be used as
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+  input, as "restriction table" in  \code{\link{allFitnessEffects}}.
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+
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 }
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 \author{Ramon Diaz-Uriarte}
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@@ -66,6 +89,8 @@ multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root")
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 (a1 <- simOGraph(10))
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 library(graph) ## for simple plotting
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 plot(as(a1, "graphNEL"))
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+
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+simOGraph(3, geneNames = LETTERS[1:3])
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 }
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 \keyword{ graphs }
Browse code

v. 1.99.0

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@105089 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 17/06/2015 17:17:55
Showing 1 changed files
man/simOGraph.Rd
History View file @ e693f15
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new file mode 100644
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@@ -0,0 +1,72 @@
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+\name{simOGraph}
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+\alias{simOGraph}
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+\title{
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+  Simulate oncogenetic/CBN/XMPN DAGs.
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+}
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+\description{
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+  Simulate DAGs that represent restrictions in the accumulation of mutations.
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+}
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+\usage{
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+simOGraph(n, h = 4, conjunction = TRUE, nparents = 3,
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+multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root")
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+}
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+
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+\arguments{
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+  \item{n}{
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+    Number of nodes, or edges, in the graph. Like the number of genes.
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+}
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+  \item{h}{
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+    Approximate height of the graph. See details.
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+  }
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+  \item{conjunction}{
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+    If TRUE, conjunctions (i.e., multiple parents for a node) are allowed.
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+}
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+\item{nparents}{
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+  Maximum number of parents of a node, when \code{conjunction} is TRUE.
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+}
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+\item{multilevelParent}{
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+  Can a node have parents at different heights (i.e., parents that are
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+  at different distance from the root node)?
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+}
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+  \item{removeDirectIndirect}{
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+    Ensure that no two nodes are connected both directly (i.e., with an
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+  edge between them) and indirectly, through intermediate nodes. If
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+  TRUE, the direct connections are removed from the graph starting from
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+  the bottom.
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+}
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+\item{rootName}{
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+  The name you want to give the "Root" node.
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+
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+}
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+}
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+\details{
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+  This is a simple, heuristic procedure for generating graphs of
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+  restrictions that seem compatible with published trees in the
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+  oncogenetic literature.
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+
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+  The basic procedure is as follows: nodes (argument \code{n}) are split
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+  into approximately equally sized \code{h} groups, and then each node
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+  from a level is connected to nodes chosen randomly from nodes of the
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+  remaing superior (i.e., closer to the Root) levels. The number of
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+  edges comes from a uniform distribution between 1 and \code{nparents}.
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+
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+  The actual depth of the graph can be smaller than \code{h} because
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+  nodes from a level might be connected to superior levels skipping
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+  intermediate ones.
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+
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+  See the vignette for further discussion about arguments.
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+
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+}
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+\value{
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+  An adjacency matrix for a directed graph.
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+}
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+\author{Ramon Diaz-Uriarte}
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+
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+\examples{
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+(a1 <- simOGraph(10))
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+library(graph) ## for simple plotting
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+plot(as(a1, "graphNEL"))
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+}
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+
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+\keyword{ graphs }
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+\keyword{ datagen }