Ahmed Mohamed authored on 01/03/2019 06:31:42 | ... | ... |
@@ -28,11 +28,11 @@ Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker
|
| 28 | 28 |
# Calculate Pearson's correlation. |
| 29 | 29 |
data(ex_microarray) # Part of ALL dataset. |
| 30 | 30 |
rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph, |
| 31 |
- weight.method = "cor", use.attr="miriam.uniprot", |
|
| 31 |
+ weight.method = "cor", use.attr="miriam.uniprot", |
|
| 32 | 32 |
y=factor(colnames(ex_microarray)), bootstrap = FALSE) |
| 33 | 33 |
|
| 34 | 34 |
## Get ranked paths using probabilistic shortest paths. |
| 35 |
- ranked.p <- pathRanker(rgraph, method="prob.shortest.path", |
|
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+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path", |
|
| 36 | 36 |
K=20, minPathSize=6) |
| 37 | 37 |
|
| 38 | 38 |
## Get the subnetwork of paths in reaction graph. |
| ... | ... |
@@ -41,12 +41,12 @@ Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker
|
| 41 | 41 |
## Get the subnetwork of paths in the original metabolic graph. |
| 42 | 42 |
metabolic.sub <- getPathsAsEIDs(ranked.p, ex_sbml) |
| 43 | 43 |
|
| 44 |
-} |
|
| 45 |
-\author{
|
|
| 46 |
-Ahmed Mohamed |
|
| 47 | 44 |
} |
| 48 | 45 |
\seealso{
|
| 49 | 46 |
Other Path ranking methods: \code{\link{getPathsAsEIDs}},
|
| 50 | 47 |
\code{\link{pathRanker}}, \code{\link{samplePaths}}
|
| 51 | 48 |
} |
| 52 |
- |
|
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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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ahmohamed authored on 19/09/2016 02:16:33 | ... | ... |
@@ -1,4 +1,5 @@ |
| 1 |
-% Generated by roxygen2 (4.0.1): do not edit by hand |
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| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/pathRank.R |
|
| 2 | 3 |
\name{extractPathNetwork}
|
| 3 | 4 |
\alias{extractPathNetwork}
|
| 4 | 5 |
\title{Creates a subnetwork from a ranked path list}
|
| ... | ... |
@@ -18,7 +19,7 @@ labels (sample categories), a subnetwork is returned for each label. |
| 18 | 19 |
Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker}}.
|
| 19 | 20 |
} |
| 20 | 21 |
\examples{
|
| 21 |
-## Prepare a weighted reaction network. |
|
| 22 |
+ ## Prepare a weighted reaction network. |
|
| 22 | 23 |
## Conver a metabolic network to a reaction network. |
| 23 | 24 |
data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism. |
| 24 | 25 |
rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE) |
| ... | ... |
@@ -27,11 +28,11 @@ Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker
|
| 27 | 28 |
# Calculate Pearson's correlation. |
| 28 | 29 |
data(ex_microarray) # Part of ALL dataset. |
| 29 | 30 |
rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph, |
| 30 |
- weight.method = "cor", use.attr="miriam.uniprot", |
|
| 31 |
+ weight.method = "cor", use.attr="miriam.uniprot", |
|
| 31 | 32 |
y=factor(colnames(ex_microarray)), bootstrap = FALSE) |
| 32 | 33 |
|
| 33 | 34 |
## Get ranked paths using probabilistic shortest paths. |
| 34 |
- ranked.p <- pathRanker(rgraph, method="prob.shortest.path", |
|
| 35 |
+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path", |
|
| 35 | 36 |
K=20, minPathSize=6) |
| 36 | 37 |
|
| 37 | 38 |
## Get the subnetwork of paths in reaction graph. |
| ... | ... |
@@ -39,12 +40,13 @@ Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker
|
| 39 | 40 |
|
| 40 | 41 |
## Get the subnetwork of paths in the original metabolic graph. |
| 41 | 42 |
metabolic.sub <- getPathsAsEIDs(ranked.p, ex_sbml) |
| 43 |
+ |
|
| 42 | 44 |
} |
| 43 | 45 |
\author{
|
| 44 | 46 |
Ahmed Mohamed |
| 45 | 47 |
} |
| 46 | 48 |
\seealso{
|
| 47 |
-Other Path ranking methods: \code{\link{getPathsAsEIDs}};
|
|
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- \code{\link{pathRanker}}; \code{\link{samplePaths}}
|
|
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+Other Path ranking methods: \code{\link{getPathsAsEIDs}},
|
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+ \code{\link{pathRanker}}, \code{\link{samplePaths}}
|
|
| 49 | 51 |
} |
| 50 | 52 |
|
Ahmed Mohamed authored on 04/07/2015 00:36:26 added plotCytoscapeGML , Geneset export formats, bug fixes
amfy10 authored on 28/06/2014 15:36:04 | ... | ... |
@@ -1,3 +1,4 @@ |
| 1 |
+% Generated by roxygen2 (4.0.1): do not edit by hand |
|
| 1 | 2 |
\name{extractPathNetwork}
|
| 2 | 3 |
\alias{extractPathNetwork}
|
| 3 | 4 |
\title{Creates a subnetwork from a ranked path list}
|
| ... | ... |
@@ -5,19 +6,16 @@ |
| 5 | 6 |
extractPathNetwork(paths, graph) |
| 6 | 7 |
} |
| 7 | 8 |
\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}}.}
|
|
| 10 | 10 |
|
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- \item{graph}{A annotated igraph object.}
|
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+\item{graph}{A annotated igraph object.}
|
|
| 12 | 12 |
} |
| 13 | 13 |
\value{
|
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-A subnetwork from all paths provided. If paths are computed |
|
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-for several labels (sample categories), a subnetwork is |
|
| 16 |
-returned for each label. |
|
| 14 |
+A subnetwork from all paths provided. If paths are computed for several |
|
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+labels (sample categories), a subnetwork is returned for each label. |
|
| 17 | 16 |
} |
| 18 | 17 |
\description{
|
| 19 |
-Creates a subnetwork from a ranked path list generated by |
|
| 20 |
-\code{\link{pathRanker}}.
|
|
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+Creates a subnetwork from a ranked path list generated by \code{\link{pathRanker}}.
|
|
| 21 | 19 |
} |
| 22 | 20 |
\examples{
|
| 23 | 21 |
## Prepare a weighted reaction network. |
| ... | ... |
@@ -47,6 +45,6 @@ Ahmed Mohamed |
| 47 | 45 |
} |
| 48 | 46 |
\seealso{
|
| 49 | 47 |
Other Path ranking methods: \code{\link{getPathsAsEIDs}};
|
| 50 |
-\code{\link{pathRanker}}; \code{\link{samplePaths}}
|
|
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+ \code{\link{pathRanker}}; \code{\link{samplePaths}}
|
|
| 51 | 49 |
} |
| 52 | 50 |
|
amfy10 authored on 10/03/2014 12:16:44 | 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,52 @@ |
| 1 |
+\name{extractPathNetwork}
|
|
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+\alias{extractPathNetwork}
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|
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+\title{Creates a subnetwork from a ranked path list}
|
|
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+\usage{
|
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+extractPathNetwork(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 subnetwork from all paths provided. If paths are computed |
|
| 15 |
+for several labels (sample categories), a subnetwork is |
|
| 16 |
+returned for each label. |
|
| 17 |
+} |
|
| 18 |
+\description{
|
|
| 19 |
+Creates a subnetwork from a ranked path list generated by |
|
| 20 |
+\code{\link{pathRanker}}.
|
|
| 21 |
+} |
|
| 22 |
+\examples{
|
|
| 23 |
+## Prepare a weighted reaction network. |
|
| 24 |
+ ## Conver a metabolic network to a reaction network. |
|
| 25 |
+ data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism. |
|
| 26 |
+ rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE) |
|
| 27 |
+ |
|
| 28 |
+ ## Assign edge weights based on Affymetrix attributes and microarray dataset. |
|
| 29 |
+ # Calculate Pearson's correlation. |
|
| 30 |
+ data(ex_microarray) # Part of ALL dataset. |
|
| 31 |
+ rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph, |
|
| 32 |
+ weight.method = "cor", use.attr="miriam.uniprot", |
|
| 33 |
+ y=factor(colnames(ex_microarray)), bootstrap = FALSE) |
|
| 34 |
+ |
|
| 35 |
+ ## Get ranked paths using probabilistic shortest paths. |
|
| 36 |
+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path", |
|
| 37 |
+ K=20, minPathSize=6) |
|
| 38 |
+ |
|
| 39 |
+ ## Get the subnetwork of paths in reaction graph. |
|
| 40 |
+ reaction.sub <- getPathsAsEIDs(ranked.p, rgraph) |
|
| 41 |
+ |
|
| 42 |
+ ## Get the subnetwork of paths in the original metabolic graph. |
|
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+ metabolic.sub <- getPathsAsEIDs(ranked.p, ex_sbml) |
|
| 44 |
+} |
|
| 45 |
+\author{
|
|
| 46 |
+Ahmed Mohamed |
|
| 47 |
+} |
|
| 48 |
+\seealso{
|
|
| 49 |
+Other Path ranking methods: \code{\link{getPathsAsEIDs}};
|
|
| 50 |
+\code{\link{pathRanker}}; \code{\link{samplePaths}}
|
|
| 51 |
+} |
|
| 52 |
+ |