#### 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
Showing 1 changed files
 ... ... @@ -84,7 +84,10 @@ sh. See \code{\link{allFitnessEffects}}} 84 84  input, as "restriction table" in \code{\link{allFitnessEffects}}. 85 85   86 86  } 87 -\author{Ramon Diaz-Uriarte} 87 +\author{Ramon Diaz-Uriarte. Code for transitive closure taken from the 88 + nem package, whose authors are Holger Froehlich, Florian Markowetz, 89 + Achim Tresch, Theresa Niederberger, Christian Bender, Matthias Maneck, 90 + Claudio Lottaz, Tim Beissbarth} 88 91   89 92  \examples{ 90 93  (a1 <- simOGraph(10))

#### 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
Showing 1 changed files
 ... ... @@ -34,8 +34,9 @@ s = 0.1, sh = -0.1, typeDep = "AND") 34 34  \item{removeDirectIndirect}{ 35 35  Ensure that no two nodes are connected both directly (i.e., with an 36 36  edge between them) and indirectly, through intermediate nodes. If 37 - TRUE, the direct connections are removed from the graph starting from 38 - the bottom. 37 + TRUE, we return the transitive reduction of the DAG. 38 + %% the final DAG returned is the transitive reduction of thethe direct 39 + %% connections are removed from the graph starting from the bottom. 39 40  } 40 41  \item{rootName}{ 41 42  The name you want to give the "Root" node.

#### 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.

 ... ... @@ -7,8 +7,11 @@ 7 7  Simulate DAGs that represent restrictions in the accumulation of mutations. 8 8  } 9 9  \usage{ 10 -simOGraph(n, h = 4, conjunction = TRUE, nparents = 3, 11 -multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root") 10 +simOGraph(n, h = ifelse(n >= 4, 4, n), conjunction = TRUE, nparents = 3, 11 +multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root", 12 +geneNames = seq.int(n), out = c("adjmat", "rT"), 13 +s = 0.1, sh = -0.1, typeDep = "AND") 14 + 12 15  } 13 16   14 17  \arguments{ ... ... @@ -36,9 +39,27 @@ multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root") 36 39  } 37 40  \item{rootName}{ 38 41  The name you want to give the "Root" node. 42 +} 39 43   44 +\item{geneNames}{ 45 + The names you want to give the the non-root nodes. 40 46  } 47 + 48 + 49 +\item{out}{Whether the ouptut should be an adjacency matrix or a 50 + "restriction table", as used in \code{\link{allFitnessEffects}}.} 51 + 52 +\item{s}{If using as output a restriction, the default value for s. See 53 +\code{\link{allFitnessEffects}}.} 54 + 55 +\item{sh}{If using as output a restriction, the default value for 56 +sh. See \code{\link{allFitnessEffects}}} 57 + 58 +\item{typeDep}{If using as output a restriction, the default value for 59 +"typeDep". See \code{\link{allFitnessEffects}}} 60 + 41 61  } 62 + 42 63  \details{ 43 64  This is a simple, heuristic procedure for generating graphs of 44 65  restrictions that seem compatible with published trees in the ... ... @@ -58,7 +79,9 @@ multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root") 58 79   59 80  } 60 81  \value{ 61 - An adjacency matrix for a directed graph. 82 + An adjacency matrix for a directed graph or a data frame to be used as 83 + input, as "restriction table" in \code{\link{allFitnessEffects}}. 84 + 62 85  } 63 86  \author{Ramon Diaz-Uriarte} 64 87   ... ... @@ -66,6 +89,8 @@ multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root") 66 89  (a1 <- simOGraph(10)) 67 90  library(graph) ## for simple plotting 68 91  plot(as(a1, "graphNEL")) 92 + 93 +simOGraph(3, geneNames = LETTERS[1:3]) 69 94  } 70 95   71 96  \keyword{ graphs }
 1 1 new file mode 100644 ... ... @@ -0,0 +1,72 @@ 1 +\name{simOGraph} 2 +\alias{simOGraph} 3 +\title{ 4 + Simulate oncogenetic/CBN/XMPN DAGs. 5 +} 6 +\description{ 7 + Simulate DAGs that represent restrictions in the accumulation of mutations. 8 +} 9 +\usage{ 10 +simOGraph(n, h = 4, conjunction = TRUE, nparents = 3, 11 +multilevelParent = TRUE, removeDirectIndirect = TRUE, rootName = "Root") 12 +} 13 + 14 +\arguments{ 15 + \item{n}{ 16 + Number of nodes, or edges, in the graph. Like the number of genes. 17 +} 18 + \item{h}{ 19 + Approximate height of the graph. See details. 20 + } 21 + \item{conjunction}{ 22 + If TRUE, conjunctions (i.e., multiple parents for a node) are allowed. 23 +} 24 +\item{nparents}{ 25 + Maximum number of parents of a node, when \code{conjunction} is TRUE. 26 +} 27 +\item{multilevelParent}{ 28 + Can a node have parents at different heights (i.e., parents that are 29 + at different distance from the root node)? 30 +} 31 + \item{removeDirectIndirect}{ 32 + Ensure that no two nodes are connected both directly (i.e., with an 33 + edge between them) and indirectly, through intermediate nodes. If 34 + TRUE, the direct connections are removed from the graph starting from 35 + the bottom. 36 +} 37 +\item{rootName}{ 38 + The name you want to give the "Root" node. 39 + 40 +} 41 +} 42 +\details{ 43 + This is a simple, heuristic procedure for generating graphs of 44 + restrictions that seem compatible with published trees in the 45 + oncogenetic literature. 46 + 47 + The basic procedure is as follows: nodes (argument \code{n}) are split 48 + into approximately equally sized \code{h} groups, and then each node 49 + from a level is connected to nodes chosen randomly from nodes of the 50 + remaing superior (i.e., closer to the Root) levels. The number of 51 + edges comes from a uniform distribution between 1 and \code{nparents}. 52 + 53 + The actual depth of the graph can be smaller than \code{h} because 54 + nodes from a level might be connected to superior levels skipping 55 + intermediate ones. 56 + 57 + See the vignette for further discussion about arguments.  58 + 59 +} 60 +\value{ 61 + An adjacency matrix for a directed graph. 62 +} 63 +\author{Ramon Diaz-Uriarte} 64 + 65 +\examples{ 66 +(a1 <- simOGraph(10)) 67 +library(graph) ## for simple plotting 68 +plot(as(a1, "graphNEL")) 69 +} 70 + 71 +\keyword{ graphs } 72 +\keyword{ datagen }