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Docs update 1.19

Ahmed Mohamed authored on 01/03/2019 06:31:42
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@@ -29,25 +29,25 @@ edges on a metabolic network).
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  # Calculate Pearson's correlation.
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 	data(ex_microarray)	# Part of ALL dataset.
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 	rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph,
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-		weight.method = "cor", use.attr="miriam.uniprot", 
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+		weight.method = "cor", use.attr="miriam.uniprot",
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 		y=factor(colnames(ex_microarray)), bootstrap = FALSE)
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 	## Get ranked paths using probabilistic shortest paths.
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- ranked.p <- pathRanker(rgraph, method="prob.shortest.path", 
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+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
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 					K=20, minPathSize=6)
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- 
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+
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 	## Get the edge ids along paths in the reaction graph.
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 	path.eids <- getPathsAsEIDs(ranked.p, rgraph)
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 	## Get the edge ids along paths in the original metabolic graph.
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 	path.eids <- getPathsAsEIDs(ranked.p, ex_sbml)
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-}
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-\author{
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-Ahmed Mohamed
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 }
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 \seealso{
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 Other Path ranking methods: \code{\link{extractPathNetwork}},
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   \code{\link{pathRanker}}, \code{\link{samplePaths}}
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 }
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-
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+\author{
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+Ahmed Mohamed
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+}
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+\concept{Path ranking methods}
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update docs using roxygen2

ahmohamed authored on 19/09/2016 02:16:33
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@@ -1,4 +1,5 @@
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-% Generated by roxygen2 (4.0.1): do not edit by hand
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/pathRank.R
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 \name{getPathsAsEIDs}
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 \alias{getPathsAsEIDs}
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 \title{Convert a ranked path list to edge ids of a graph}
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@@ -19,7 +20,7 @@ a different representation (for example matching path from a reaction network to
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 edges on a metabolic network).
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 }
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 \examples{
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-## Prepare a weighted reaction network.
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+	## Prepare a weighted reaction network.
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 	## Conver a metabolic network to a reaction network.
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  data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
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  rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)
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@@ -28,24 +29,25 @@ edges on a metabolic network).
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  # Calculate Pearson's correlation.
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 	data(ex_microarray)	# Part of ALL dataset.
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 	rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph,
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-		weight.method = "cor", use.attr="miriam.uniprot",
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+		weight.method = "cor", use.attr="miriam.uniprot", 
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 		y=factor(colnames(ex_microarray)), bootstrap = FALSE)
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 	## Get ranked paths using probabilistic shortest paths.
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- ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
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+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path", 
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 					K=20, minPathSize=6)
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-
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+ 
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 	## Get the edge ids along paths in the reaction graph.
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 	path.eids <- getPathsAsEIDs(ranked.p, rgraph)
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 	## Get the edge ids along paths in the original metabolic graph.
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 	path.eids <- getPathsAsEIDs(ranked.p, ex_sbml)
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+
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 }
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 \author{
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 Ahmed Mohamed
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 }
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 \seealso{
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-Other Path ranking methods: \code{\link{extractPathNetwork}};
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-  \code{\link{pathRanker}}; \code{\link{samplePaths}}
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+Other Path ranking methods: \code{\link{extractPathNetwork}},
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+  \code{\link{pathRanker}}, \code{\link{samplePaths}}
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 }
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empty commit

Ahmed Mohamed authored on 04/07/2015 00:36:26
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old mode 100644
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new mode 100755
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Updates

added plotCytoscapeGML , Geneset export formats, bug fixes

amfy10 authored on 28/06/2014 15:36:04
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@@ -1,3 +1,4 @@
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+% Generated by roxygen2 (4.0.1): do not edit by hand
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 \name{getPathsAsEIDs}
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 \alias{getPathsAsEIDs}
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 \title{Convert a ranked path list to edge ids of a graph}
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@@ -5,19 +6,17 @@
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 getPathsAsEIDs(paths, graph)
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 }
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 \arguments{
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-  \item{paths}{The paths extracted by
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-  \code{\link{pathRanker}}.}
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+\item{paths}{The paths extracted by \code{\link{pathRanker}}.}
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-  \item{graph}{A annotated igraph object.}
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+\item{graph}{A annotated igraph object.}
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 }
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 \value{
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 A list of edge ids on the provided graph.
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 }
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 \description{
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-Convert a ranked path list to Edge ids of a graph, where
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-paths can come from a different representation (for example
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-matching path from a reaction network to edges on a
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-metabolic network).
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+Convert a ranked path list to Edge ids of a graph, where paths can come from
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+a different representation (for example matching path from a reaction network to
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+edges on a metabolic network).
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 }
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 \examples{
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 ## Prepare a weighted reaction network.
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@@ -46,8 +45,7 @@ metabolic network).
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 Ahmed Mohamed
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 }
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 \seealso{
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-Other Path ranking methods:
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-\code{\link{extractPathNetwork}}; \code{\link{pathRanker}};
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-\code{\link{samplePaths}}
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+Other Path ranking methods: \code{\link{extractPathNetwork}};
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+  \code{\link{pathRanker}}; \code{\link{samplePaths}}
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 }
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Release 0.99.0 Biocunductor submission

amfy10 authored on 10/03/2014 12:16:44
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new file mode 100644
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@@ -0,0 +1,53 @@
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+\name{getPathsAsEIDs}
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+\alias{getPathsAsEIDs}
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+\title{Convert a ranked path list to edge ids of a graph}
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+\usage{
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+getPathsAsEIDs(paths, graph)
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+}
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+\arguments{
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+  \item{paths}{The paths extracted by
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+  \code{\link{pathRanker}}.}
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+
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+  \item{graph}{A annotated igraph object.}
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+}
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+\value{
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+A list of edge ids on the provided graph.
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+}
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+\description{
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+Convert a ranked path list to Edge ids of a graph, where
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+paths can come from a different representation (for example
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+matching path from a reaction network to edges on a
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+metabolic network).
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+}
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+\examples{
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+## Prepare a weighted reaction network.
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+	## Conver a metabolic network to a reaction network.
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+ data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
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+ rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)
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+
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+	## Assign edge weights based on Affymetrix attributes and microarray dataset.
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+ # Calculate Pearson's correlation.
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+	data(ex_microarray)	# Part of ALL dataset.
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+	rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph,
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+		weight.method = "cor", use.attr="miriam.uniprot",
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+		y=factor(colnames(ex_microarray)), bootstrap = FALSE)
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+
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+	## Get ranked paths using probabilistic shortest paths.
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+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
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+					K=20, minPathSize=6)
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+
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+	## Get the edge ids along paths in the reaction graph.
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+	path.eids <- getPathsAsEIDs(ranked.p, rgraph)
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+
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+	## Get the edge ids along paths in the original metabolic graph.
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+	path.eids <- getPathsAsEIDs(ranked.p, ex_sbml)
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+}
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+\author{
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+Ahmed Mohamed
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+}
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+\seealso{
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+Other Path ranking methods:
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+\code{\link{extractPathNetwork}}; \code{\link{pathRanker}};
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+\code{\link{samplePaths}}
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+}
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+