1. NetPathMiner
  2. man
  3. predictPathCluster.Rd
Browse code

Docs update 1.19

Ahmed Mohamed authored on 01/03/2019 06:31:42
Showing1 changed files
man/predictPathCluster.Rd
History View file @087265c
... ... 
@@ -34,21 +34,16 @@ Predicts new paths given a pathCluster model.
34 34 
 		weight.method = "cor", use.attr="miriam.uniprot", bootstrap = FALSE)
35 35
36 36 
 	## Get ranked paths using probabilistic shortest paths.
37 
- ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
37 
+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
38 38 
 					K=20, minPathSize=8)
39 
-
40 
-	## Convert paths to binary matrix.
39 
+
40 
+	## Convert paths to binary matrix.
41 41 
 	ybinpaths <- pathsToBinary(ranked.p)
42 42 
 	p.cluster <- pathCluster(ybinpaths, M=2)
43 43
44 44 
 	## just an example of how to predict cluster membership.
45 45 
 	pclust.pred <- predictPathCluster(p.cluster,ybinpaths$paths)
46 
-
47 
-}
48 
-\author{
49 
-Ichigaku Takigawa
50 46
51 
-Timothy Hancock
52 47 
 }
53 48 
 \seealso{
54 49 
 Other Path clustering & classification methods: \code{\link{pathClassifier}},
... ... 
@@ -59,4 +54,9 @@ Other Path clustering & classification methods: \code{\link{pathClassifier}},
59 54 
   \code{\link{plotPathCluster}},
60 55 
   \code{\link{predictPathClassifier}}
61 56 
 }
57 
+\author{
58 
+Ichigaku Takigawa
62 59
60 
+Timothy Hancock
61 
+}
62 
+\concept{Path clustering & classification methods}
Browse code

update docs using roxygen2

ahmohamed authored on 19/09/2016 02:16:33
Showing1 changed files
man/predictPathCluster.Rd
History View file @2aadfaf
... ... 
@@ -1,4 +1,5 @@
1 
-% Generated by roxygen2 (4.0.1): do not edit by hand
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/pathCluster.R
2 3 
 \name{predictPathCluster}
3 4 
 \alias{predictPathCluster}
4 5 
 \title{Predicts new paths given a pathCluster model}
... ... 
@@ -21,7 +22,7 @@ A list with the following elements:
21 22 
 Predicts new paths given a pathCluster model.
22 23 
 }
23 24 
 \examples{
24 
-## Prepare a weighted reaction network.
25 
+	## Prepare a weighted reaction network.
25 26 
 	## Conver a metabolic network to a reaction network.
26 27 
  data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
27 28 
  rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)
... ... 
@@ -33,15 +34,16 @@ Predicts new paths given a pathCluster model.
33 34 
 		weight.method = "cor", use.attr="miriam.uniprot", bootstrap = FALSE)
34 35
35 36 
 	## Get ranked paths using probabilistic shortest paths.
36 
- ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
37 
+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
37 38 
 					K=20, minPathSize=8)
38 
-
39 
-	## Convert paths to binary matrix.
39 
+
40 
+	## Convert paths to binary matrix.
40 41 
 	ybinpaths <- pathsToBinary(ranked.p)
41 42 
 	p.cluster <- pathCluster(ybinpaths, M=2)
42 43
43 44 
 	## just an example of how to predict cluster membership.
44 45 
 	pclust.pred <- predictPathCluster(p.cluster,ybinpaths$paths)
46 
+
45 47 
 }
46 48 
 \author{
47 49 
 Ichigaku Takigawa
... ... 
@@ -49,14 +51,12 @@ Ichigaku Takigawa
49 51 
 Timothy Hancock
50 52 
 }
51 53 
 \seealso{
52 
-Other Path clustering & classification methods: \code{\link{pathClassifier}};
53 
-  \code{\link{pathCluster}}; \code{\link{pathsToBinary}};
54 
-  \code{\link{plotClassifierROC}};
54 
+Other Path clustering & classification methods: \code{\link{pathClassifier}},
55 
+  \code{\link{pathCluster}}, \code{\link{pathsToBinary}},
56 
+  \code{\link{plotClassifierROC}},
55 57 
   \code{\link{plotClusterMatrix}},
56 
-  \code{\link{plotClusterProbs}},
57 
-  \code{\link{plotClusters}};
58 
-  \code{\link{plotPathClassifier}};
59 
-  \code{\link{plotPathCluster}};
58 
+  \code{\link{plotPathClassifier}},
59 
+  \code{\link{plotPathCluster}},
60 60 
   \code{\link{predictPathClassifier}}
61 61 
 }
62 62
Browse code

empty commit

Ahmed Mohamed authored on 04/07/2015 00:36:26
Showing1 changed files
man/predictPathCluster.Rd
History View file @555ec75
1 1 
old mode 100644
2 2 
new mode 100755
Browse code

Updates

added plotCytoscapeGML , Geneset export formats, bug fixes

amfy10 authored on 28/06/2014 15:36:04
Showing1 changed files
man/predictPathCluster.Rd
History View file @a6b3c97
... ... 
@@ -1,3 +1,4 @@
1 
+% Generated by roxygen2 (4.0.1): do not edit by hand
1 2 
 \name{predictPathCluster}
2 3 
 \alias{predictPathCluster}
3 4 
 \title{Predicts new paths given a pathCluster model}
... ... 
@@ -5,19 +6,16 @@
5 6 
 predictPathCluster(pfit, newdata)
6 7 
 }
7 8 
 \arguments{
8 
-  \item{pfit}{The pathway cluster model trained by
9 
-  \code{\link{pathCluster}} or
10 
-  \code{\link{pathClassifier}}.}
9 
+\item{pfit}{The pathway cluster model trained by \code{\link{pathCluster}} or \code{\link{pathClassifier}}.}
11 10
12 
-  \item{newdata}{The binary pathway dataset to be assigned
13 
-  a cluster label.}
11 
+\item{newdata}{The binary pathway dataset to be assigned a cluster label.}
14 12 
 }
15 13 
 \value{
16 
-A list with the following elements: \tabular{ll}{
17 
-\code{labels} \tab a vector indicating the 3M cluster
18 
-membership. \cr \code{posterior.probs} \tab a matrix of
19 
-posterior probabilities for each path belonging to each
20 
-cluster. }
14 
+A list with the following elements:
15 
+\tabular{ll}{
16 
+\code{labels} \tab a vector indicating the 3M cluster membership. \cr
17 
+\code{posterior.probs} \tab a matrix of posterior probabilities for each path belonging to each cluster.
18 
+}
21 19 
 }
22 20 
 \description{
23 21 
 Predicts new paths given a pathCluster model.
... ... 
@@ -51,14 +49,14 @@ Ichigaku Takigawa
51 49 
 Timothy Hancock
52 50 
 }
53 51 
 \seealso{
54 
-Other Path clustering & classification methods:
55 
-\code{\link{pathClassifier}}; \code{\link{pathCluster}};
56 
-\code{\link{pathsToBinary}};
57 
-\code{\link{plotClassifierROC}};
58 
-\code{\link{plotClusterMatrix}},
59 
-\code{\link{plotClusterProbs}}, \code{\link{plotClusters}};
60 
-\code{\link{plotPathClassifier}};
61 
-\code{\link{plotPathCluster}};
62 
-\code{\link{predictPathClassifier}}
52 
+Other Path clustering & classification methods: \code{\link{pathClassifier}};
53 
+  \code{\link{pathCluster}}; \code{\link{pathsToBinary}};
54 
+  \code{\link{plotClassifierROC}};
55 
+  \code{\link{plotClusterMatrix}},
56 
+  \code{\link{plotClusterProbs}},
57 
+  \code{\link{plotClusters}};
58 
+  \code{\link{plotPathClassifier}};
59 
+  \code{\link{plotPathCluster}};
60 
+  \code{\link{predictPathClassifier}}
63 61 
 }
64 62
Browse code

0.99.3

Bioconductor, No errors/warnings.

amfy10 authored on 09/04/2014 09:29:08
Showing1 changed files
man/predictPathCluster.Rd
History View file @572c4aa
... ... 
@@ -36,11 +36,11 @@ Predicts new paths given a pathCluster model.
36 36
37 37 
 	## Get ranked paths using probabilistic shortest paths.
38 38 
  ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
39 
-					K=20, minPathSize=6)
39 
+					K=20, minPathSize=8)
40 40
41 41 
 	## Convert paths to binary matrix.
42 42 
 	ybinpaths <- pathsToBinary(ranked.p)
43 
-	p.cluster <- pathCluster(ybinpaths, M=3)
43 
+	p.cluster <- pathCluster(ybinpaths, M=2)
44 44
45 45 
 	## just an example of how to predict cluster membership.
46 46 
 	pclust.pred <- predictPathCluster(p.cluster,ybinpaths$paths)
Browse code

Release 0.99.0 Biocunductor submission

amfy10 authored on 10/03/2014 12:16:44
Showing1 changed files
man/predictPathCluster.Rd
History View file @96e22bf
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,64 @@
1 
+\name{predictPathCluster}
2 
+\alias{predictPathCluster}
3 
+\title{Predicts new paths given a pathCluster model}
4 
+\usage{
5 
+predictPathCluster(pfit, newdata)
6 
+}
7 
+\arguments{
8 
+  \item{pfit}{The pathway cluster model trained by
9 
+  \code{\link{pathCluster}} or
10 
+  \code{\link{pathClassifier}}.}
11 
+
12 
+  \item{newdata}{The binary pathway dataset to be assigned
13 
+  a cluster label.}
14 
+}
15 
+\value{
16 
+A list with the following elements: \tabular{ll}{
17 
+\code{labels} \tab a vector indicating the 3M cluster
18 
+membership. \cr \code{posterior.probs} \tab a matrix of
19 
+posterior probabilities for each path belonging to each
20 
+cluster. }
21 
+}
22 
+\description{
23 
+Predicts new paths given a pathCluster model.
24 
+}
25 
+\examples{
26 
+## Prepare a weighted reaction network.
27 
+	## Conver a metabolic network to a reaction network.
28 
+ data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
29 
+ rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)
30 
+
31 
+	## Assign edge weights based on Affymetrix attributes and microarray dataset.
32 
+ # Calculate Pearson's correlation.
33 
+	data(ex_microarray)	# Part of ALL dataset.
34 
+	rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph,
35 
+		weight.method = "cor", use.attr="miriam.uniprot", bootstrap = FALSE)
36 
+
37 
+	## Get ranked paths using probabilistic shortest paths.
38 
+ ranked.p <- pathRanker(rgraph, method="prob.shortest.path",
39 
+					K=20, minPathSize=6)
40 
+
41 
+	## Convert paths to binary matrix.
42 
+	ybinpaths <- pathsToBinary(ranked.p)
43 
+	p.cluster <- pathCluster(ybinpaths, M=3)
44 
+
45 
+	## just an example of how to predict cluster membership.
46 
+	pclust.pred <- predictPathCluster(p.cluster,ybinpaths$paths)
47 
+}
48 
+\author{
49 
+Ichigaku Takigawa
50 
+
51 
+Timothy Hancock
52 
+}
53 
+\seealso{
54 
+Other Path clustering & classification methods:
55 
+\code{\link{pathClassifier}}; \code{\link{pathCluster}};
56 
+\code{\link{pathsToBinary}};
57 
+\code{\link{plotClassifierROC}};
58 
+\code{\link{plotClusterMatrix}},
59 
+\code{\link{plotClusterProbs}}, \code{\link{plotClusters}};
60 
+\code{\link{plotPathClassifier}};
61 
+\code{\link{plotPathCluster}};
62 
+\code{\link{predictPathClassifier}}
63 
+}
64 
+