1. Rtreemix
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  3. gps-methods.Rd
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docs update

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@41371 bc3139a8-67e5-0310-9ffc-ced21a209358

Jasmina Bogojeska authored on 27/08/2009 09:08:41
Showing 1 changed files
man/gps-methods.Rd
History View file @ ca550c2
... ... 
@@ -22,13 +22,7 @@
22 22 
 }
23 23
24 24 
 \usage{
25 
-gps(model, ...)
26 
-
27 
-\method{gps}{model, data}(model, data, sampling.mode = "exponential",
28 
-                         sampling.param = 1, no.sim = 10, seed = (-1))
29 
-
30 
-\method{gps}{model}(model, sampling.mode = "exponential",
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-                    sampling.param = 1, no.sim = 10, seed = (-1))
25 
+gps(model, data, \dots)
32 26 
 }
33 27
34 28 
 \section{Methods}{\describe{
... ... 
@@ -48,17 +42,19 @@ gps(model, ...)
48 42 
     containing the samples (patterns of genetic events) for which the GPS values
49 43 
     are to be calculated. The length of each of them has to be equal
50 44 
     to the number of genetic events in the \code{model}.}
51 
-  \item{sampling.mode}{A \code{character} that specifies the
45 
+  \item{\dots}{
46 
+    \code{sampling.mode} is a \code{character} that specifies the
52 47 
     sampling mode ("constant" or "exponential") used in the waiting time
53 
-    simulations. Its default value is "exponential".}
54 
-  \item{sampling.param}{A \code{numeric} that specifies the
48 
+    simulations. Its default value is "exponential".
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+    \code{sampling.param} is a \code{numeric} that specifies the
55 50 
     sampling parameter corresponding to the sampling mode given by
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-    \code{sampling.mode}. Its default value is 1.}
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-  \item{no.sim}{An \code{integer} larger than 0 giving the number of
58 
-    iterations for the waiting time simulations. Its default value is 10.}
59 
-  \item{seed}{A positive \code{integer} specifying the random generator
51 
+    \code{sampling.mode}. Its default value is 1.
52 
+    \code{no.sim} is an \code{integer} larger than 0 giving the number of
53 
+    iterations for the waiting time simulations. Its default value is 10.
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+    \code{seed} is a positive \code{integer} specifying the random generator
60 55 
     seed. Its default value is (-1) and then the time is used as a
61 
-    random generator.}
56 
+    random generator.
57 
+  }
62 58 
 }
63 59
64 60 
 \value{
... ... 
@@ -76,7 +72,7 @@ gps(model, ...)
76 72 
     The mixture model used for deriving the GPS values should not have more than
77 73 
     20 genetic events. The reason for this is that the number of all possible patterns
78 74 
     for which the GPS values are calculated during a computationally intensive simulations
79 
-    is in this case $2^{20}$. This demands too much memory.
75 
+    is in this case $2^20$. This demands too much memory.
80 76 
     The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
81 77 
     For trying out the code please copy it and uncomment it.
82 78 
 }
Browse code

modifed man files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@41283 bc3139a8-67e5-0310-9ffc-ced21a209358

Jasmina Bogojeska authored on 21/08/2009 20:38:31
Showing 1 changed files
man/gps-methods.Rd
History View file @ 8aa497e
... ... 
@@ -22,9 +22,13 @@
22 22 
 }
23 23
24 24 
 \usage{
25 
-\S4method{gps}{RtreemixModel,RtreemixData}(model, data, ...)
26 
-\S4method{gps}{RtreemixModel,matrix}(model, data, ...)
27 
-\S4method{gps}{RtreemixModel,missing}(model, data, ...)
25 
+gps(model, ...)
26 
+
27 
+\method{gps}{model, data}(model, data, sampling.mode = "exponential",
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+                         sampling.param = 1, no.sim = 10, seed = (-1))
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+
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+\method{gps}{model}(model, sampling.mode = "exponential",
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+                    sampling.param = 1, no.sim = 10, seed = (-1))
28 32 
 }
29 33
30 34 
 \section{Methods}{\describe{
... ... 
@@ -44,19 +48,17 @@
44 48 
     containing the samples (patterns of genetic events) for which the GPS values
45 49 
     are to be calculated. The length of each of them has to be equal
46 50 
     to the number of genetic events in the \code{model}.}
47 
-  \item{...}{
48 
-    \code{sampling.mode} is a \code{character} that specifies the
51 
+  \item{sampling.mode}{A \code{character} that specifies the
49 52 
     sampling mode ("constant" or "exponential") used in the waiting time
50 
-    simulations. Its default value is "exponential".
51 
-    \code{sampling.param} is a \code{numeric} that specifies the
53 
+    simulations. Its default value is "exponential".}
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+  \item{sampling.param}{A \code{numeric} that specifies the
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     sampling parameter corresponding to the sampling mode given by
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-    \code{sampling.mode}. Its default value is 1.
54 
-    \code{no.sim} is an \code{integer} larger than 0 giving the number of
55 
-    iterations for the waiting time simulations. Its default value is 10.
56 
-    \code{seed} is a positive \code{integer} specifying the random generator
56 
+    \code{sampling.mode}. Its default value is 1.}
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+  \item{no.sim}{An \code{integer} larger than 0 giving the number of
58 
+    iterations for the waiting time simulations. Its default value is 10.}
59 
+  \item{seed}{A positive \code{integer} specifying the random generator
57 60 
     seed. Its default value is (-1) and then the time is used as a
58 
-    random generator.
59 
-  }
61 
+    random generator.}
60 62 
 }
61 63
62 64 
 \value{
... ... 
@@ -74,7 +76,7 @@
74 76 
     The mixture model used for deriving the GPS values should not have more than
75 77 
     20 genetic events. The reason for this is that the number of all possible patterns
76 78 
     for which the GPS values are calculated during a computationally intensive simulations
77 
-    is in this case $2^20$. This demands too much memory.
79 
+    is in this case $2^{20}$. This demands too much memory.
78 80 
     The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
79 81 
     For trying out the code please copy it and uncomment it.
80 82 
 }
Browse code

updated man files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@31296 bc3139a8-67e5-0310-9ffc-ced21a209358

Jasmina Bogojeska authored on 24/04/2008 13:09:35
Showing 1 changed files
man/gps-methods.Rd
History View file @ d0598af
... ... 
@@ -7,6 +7,9 @@
7 7 
 \alias{gps,RtreemixModel,matrix-method}
8 8 
 \alias{gps,RtreemixModel,missing-method}
9 9
10 
+
11 
+
12 
+
10 13 
 \title{Methods for predicting the GPS of given dataset by
11 14 
   using a given mutagenetic trees mixture model}
12 15 
 \description{
... ... 
@@ -19,17 +22,17 @@
19 22 
 }
20 23
21 24 
 \usage{
22 
-\S4method{gps}{RtreemixModel,RtreemixData}(model, data, \dots)
23 
-\S4method{gps}{RtreemixModel,matrix}(model, data, \dots)
24 
-\S4method{gps}{RtreemixModel,missing}(model, data, \dots)
25 
+\S4method{gps}{RtreemixModel,RtreemixData}(model, data, ...)
26 
+\S4method{gps}{RtreemixModel,matrix}(model, data, ...)
27 
+\S4method{gps}{RtreemixModel,missing}(model, data, ...)
25 28 
 }
26 29
27 30 
 \section{Methods}{\describe{
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-    \item{model = "RtreemixModel", data = "RtreemixData", \dots}{A method for calculating
31 
+    \item{model = "RtreemixModel", data = "RtreemixData", ...}{A method for calculating
29 32 
       the GPS values of the data given as \code{RtreemixData} object.}
30 
-    \item{model = "RtreemixModel", data = "matrix", \dots}{A method for calculating
33 
+    \item{model = "RtreemixModel", data = "matrix", ...}{A method for calculating
31 34 
       the GPS values of the data given as 0-1 \code{matrix}.}
32 
-    \item{model = "RtreemixModel", data = "missing", \dots}{A method for calculating
35 
+    \item{model = "RtreemixModel", data = "missing", ...}{A method for calculating
33 36 
       the GPS values of the set of all possible patterns.}
34 37 
 }}
35 38
... ... 
@@ -41,7 +44,7 @@
41 44 
     containing the samples (patterns of genetic events) for which the GPS values
42 45 
     are to be calculated. The length of each of them has to be equal
43 46 
     to the number of genetic events in the \code{model}.}
44 
-  \item{\dots}{
47 
+  \item{...}{
45 48 
     \code{sampling.mode} is a \code{character} that specifies the
46 49 
     sampling mode ("constant" or "exponential") used in the waiting time
47 50 
     simulations. Its default value is "exponential".
... ... 
@@ -58,7 +61,7 @@
58 61
59 62 
 \value{
60 63 
   The function returns an object from the \code{RtreemixGPS} class that
61 
-  contains the calculated GPS values, the model used for the
64 
+  containes the calculated GPS values, the model used for the
62 65 
   computation, the data, and so on (see
63 66 
   \code{\link{RtreemixGPS-class}}). The GPS values are represented as a
64 67 
   \code{numeric} vector with length equal to the number of samples in \code{data}.
... ... 
@@ -71,7 +74,7 @@
71 74 
     The mixture model used for deriving the GPS values should not have more than
72 75 
     20 genetic events. The reason for this is that the number of all possible patterns
73 76 
     for which the GPS values are calculated during a computationally intensive simulations
74 
-    is in this case $2^{20}$. This demands too much memory.
77 
+    is in this case $2^20$. This demands too much memory.
75 78 
     The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
76 79 
     For trying out the code please copy it and uncomment it.
77 80 
 }
... ... 
@@ -94,19 +97,20 @@
94 97 
 #show(mod)
95 98
96 99 
 ## Create an RtreemixGPS object by calculating the GPS for all possible patterns.
97 
-#modGPS.all <- gps(model = mod, no.sim = 1000) ## time consuming computations
100 
+#modGPS.all <- gps(model = mod, no.sim = 1000) ## time consuming copmutations
98 101 
 #show(modGPS.all)
99 102
100 103 
 ## See the GPS values for all possible data.
101 
-#GPS(modGPS.all) ## time consuming computations
104 
+#GPS(modGPS.all) ## time consuming copmutations
102 105
103 106 
 ## Create an RtreemixGPS object by calculating the GPS for the data based on the model mod.
104 107 
 #modGPS <- gps(model = mod, data = data, no.sim = 1000)
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-#show(modGPS) ## time consuming computations
108 
+#show(modGPS) ## time consuming copmutations
106 109
107 110 
 ## See the GPS values for data.
108 
-#GPS(modGPS) ## time consuming computations
111 
+#GPS(modGPS) ## time consuming copmutations
109 112 
 }
110 113
114 
+
111 115 
 \keyword{methods}
112 116 
 \keyword{survival}
Browse code

Fixed man files to allow creation of Rtreemix-manual.pdf document.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@30965 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 09/04/2008 18:34:51
Showing 1 changed files
man/gps-methods.Rd
History View file @ 952f967
... ... 
@@ -7,9 +7,6 @@
7 7 
 \alias{gps,RtreemixModel,matrix-method}
8 8 
 \alias{gps,RtreemixModel,missing-method}
9 9
10 
-
11 
-
12 
-
13 10 
 \title{Methods for predicting the GPS of given dataset by
14 11 
   using a given mutagenetic trees mixture model}
15 12 
 \description{
... ... 
@@ -22,17 +19,17 @@
22 19 
 }
23 20
24 21 
 \usage{
25 
-\S4method{gps}{RtreemixModel,RtreemixData}(model, data, ...)
26 
-\S4method{gps}{RtreemixModel,matrix}(model, data, ...)
27 
-\S4method{gps}{RtreemixModel,missing}(model, data, ...)
22 
+\S4method{gps}{RtreemixModel,RtreemixData}(model, data, \dots)
23 
+\S4method{gps}{RtreemixModel,matrix}(model, data, \dots)
24 
+\S4method{gps}{RtreemixModel,missing}(model, data, \dots)
28 25 
 }
29 26
30 27 
 \section{Methods}{\describe{
31 
-    \item{model = "RtreemixModel", data = "RtreemixData", ...}{A method for calculating
28 
+    \item{model = "RtreemixModel", data = "RtreemixData", \dots}{A method for calculating
32 29 
       the GPS values of the data given as \code{RtreemixData} object.}
33 
-    \item{model = "RtreemixModel", data = "matrix", ...}{A method for calculating
30 
+    \item{model = "RtreemixModel", data = "matrix", \dots}{A method for calculating
34 31 
       the GPS values of the data given as 0-1 \code{matrix}.}
35 
-    \item{model = "RtreemixModel", data = "missing", ...}{A method for calculating
32 
+    \item{model = "RtreemixModel", data = "missing", \dots}{A method for calculating
36 33 
       the GPS values of the set of all possible patterns.}
37 34 
 }}
38 35
... ... 
@@ -44,7 +41,7 @@
44 41 
     containing the samples (patterns of genetic events) for which the GPS values
45 42 
     are to be calculated. The length of each of them has to be equal
46 43 
     to the number of genetic events in the \code{model}.}
47 
-  \item{...}{
44 
+  \item{\dots}{
48 45 
     \code{sampling.mode} is a \code{character} that specifies the
49 46 
     sampling mode ("constant" or "exponential") used in the waiting time
50 47 
     simulations. Its default value is "exponential".
... ... 
@@ -61,7 +58,7 @@
61 58
62 59 
 \value{
63 60 
   The function returns an object from the \code{RtreemixGPS} class that
64 
-  containes the calculated GPS values, the model used for the
61 
+  contains the calculated GPS values, the model used for the
65 62 
   computation, the data, and so on (see
66 63 
   \code{\link{RtreemixGPS-class}}). The GPS values are represented as a
67 64 
   \code{numeric} vector with length equal to the number of samples in \code{data}.
... ... 
@@ -74,7 +71,7 @@
74 71 
     The mixture model used for deriving the GPS values should not have more than
75 72 
     20 genetic events. The reason for this is that the number of all possible patterns
76 73 
     for which the GPS values are calculated during a computationally intensive simulations
77 
-    is in this case 2^20. This demands too much memory.
74 
+    is in this case $2^{20}$. This demands too much memory.
78 75 
     The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
79 76 
     For trying out the code please copy it and uncomment it.
80 77 
 }
... ... 
@@ -97,20 +94,19 @@
97 94 
 #show(mod)
98 95
99 96 
 ## Create an RtreemixGPS object by calculating the GPS for all possible patterns.
100 
-#modGPS.all <- gps(model = mod, no.sim = 1000) ## time consuming copmutations
97 
+#modGPS.all <- gps(model = mod, no.sim = 1000) ## time consuming computations
101 98 
 #show(modGPS.all)
102 99
103 100 
 ## See the GPS values for all possible data.
104 
-#GPS(modGPS.all) ## time consuming copmutations
101 
+#GPS(modGPS.all) ## time consuming computations
105 102
106 103 
 ## Create an RtreemixGPS object by calculating the GPS for the data based on the model mod.
107 104 
 #modGPS <- gps(model = mod, data = data, no.sim = 1000)
108 
-#show(modGPS) ## time consuming copmutations
105 
+#show(modGPS) ## time consuming computations
109 106
110 107 
 ## See the GPS values for data.
111 
-#GPS(modGPS) ## time consuming copmutations
108 
+#GPS(modGPS) ## time consuming computations
112 109 
 }
113 110
114 
-
115 111 
 \keyword{methods}
116 112 
 \keyword{survival}
Browse code

\name{confIntGPS-methods} \docType{methods}

\alias{confIntGPS}
\alias{confIntGPS-methods}
\alias{confIntGPS,RtreemixData,numeric-method}


\title{Method for calculating GPS values and their 95\% bootstrap
confidence intervals}

\description{
The method first calculates the genetic progression score (GPS) for the
patterns in a given dataset \code{data} based on a fitted mutagenetic trees
mixture model with \code{K} components. The \code{data} and \code{K}
have to be specified. Then, it derives a 95\% confidence intervals for
the GPS values with bootstrap analysis.
}

\usage{
\S4method{confIntGPS}{RtreemixData,numeric}(data, K, ...)
}

\arguments{
\item{data}{An \code{RtreemixData} object containing the samples
(patterns of genetic events) for which the GPS values and their
bootstrap confidence intervals are to be calculated. The number
of genetic events should NOT be greater than 20.}
\item{K}{An \code{integer} larger than 0 specifying the number of
branchings in the mixture model.}
\item{...}{
\code{sampling.mode} is a \code{character} that specifies the
sampling mode ("constant" or "exponential") used in the waiting time
simulations. Its default value is "exponential".
\code{sampling.param} is a \code{numeric} that specifies the
sampling parameter corresponding to the sampling mode given by
\code{sampling.mode}. Its default value is 1.
\code{no.sim} is an \code{integer} larger than 0 giving the number of
iterations for the waiting time simulation. Its default values is
10000.
\code{B} is an \code{integer} larger than 0 specifying the number of
bootstrap samples used in the bootstrap analysis. Its default value
is 1000.
\code{equal.star} is a \code{logical} specifying whether to use
equal edge weights in the noise component. The default value is
\code{TRUE}.
}
}

\value{
The function returns an object from the \code{RtreemixGPS} class that
containes the calculated GPS values, their 95\% confidence intervals,
the model used for the computation, the data, and so on (see
\code{\link{RtreemixGPS-class}}). The GPS values are represented as a
\code{numeric} vector with length equal to the number of samples in
\code{data}. Their corresponding confidence intervals are given in a
matrix with two columns.
}

\note{
The data for which the GPS values and their corresponding
confidence intervals are to be calculated should not have more
than 20 genetic events. The reason for this is that the number of all possible patterns
for which the GPS values are calculated during a computationally intensive simulations
is in this case 2^20. This demands too much memory.
The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
For trying out the code please copy it and uncomment it.
}

\author{Jasmina Bogojeska }

\seealso{
\code{\link{RtreemixGPS-class}}, \code{\link{gps-methods}},
\code{\link{RtreemixData-class}}, \code{\link{RtreemixModel-class}},
\code{\link{fit-methods}}
}

\examples{
## Create an RtreemixData object from a randomly generated RtreemixModel object.
#rand.mod <- generate(K = 2, no.events = 7, noise.tree = TRUE, prob = c(0.2, 0.8))
#data <- sim(model = rand.mod, no.draws = 400)

## Create an RtreemixGPS object by calculating GPS values for a given dataset
## and their 95\% confidence intervals using the bootstrap method.
#modGPS2 <- confIntGPS(data = data, K = 2, B = 100) ## time consuming computation
#show(modGPS2)

## See the GPS values for the object modGPS2 and their confidence intervals.
#GPS(modGPS2)
#gpsCI(modGPS2)

## See data.
#getData(modGPS2)
}

\keyword{methods}


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@30733 bc3139a8-67e5-0310-9ffc-ced21a209358

Jasmina Bogojeska authored on 28/03/2008 15:38:30
Showing 1 changed files
man/gps-methods.Rd
History View file @ 4e3040f
... ... 
@@ -74,7 +74,7 @@
74 74 
     The mixture model used for deriving the GPS values should not have more than
75 75 
     20 genetic events. The reason for this is that the number of all possible patterns
76 76 
     for which the GPS values are calculated during a computationally intensive simulations
77 
-    is in this case 2^20.
77 
+    is in this case 2^20. This demands too much memory.
78 78 
     The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
79 79 
     For trying out the code please copy it and uncomment it.
80 80 
 }
Browse code

\name{gps-methods} \docType{methods}

\alias{gps}
\alias{gps-methods}
\alias{gps,RtreemixModel,RtreemixData-method}
\alias{gps,RtreemixModel,matrix-method}
\alias{gps,RtreemixModel,missing-method}




\title{Methods for predicting the GPS of given dataset by
using a given mutagenetic trees mixture model}
\description{
These functions compute the genetic progression score (GPS) of each
sample in the given \code{data} by performing a waiting time
simulation along the branchings of the mixture model \code{model}. The
model has to be specified. If a dataset is missing a GPS for all
possible patterns is calculated. The number of events of the samples
in \code{data} equals the number of genetic events in the \code{model}.
}

\usage{
\S4method{gps}{RtreemixModel,RtreemixData}(model, data, ...)
\S4method{gps}{RtreemixModel,matrix}(model, data, ...)
\S4method{gps}{RtreemixModel,missing}(model, data, ...)
}

\section{Methods}{\describe{
\item{model = "RtreemixModel", data = "RtreemixData", ...}{A method for calculating
the GPS values of the data given as \code{RtreemixData} object.}
\item{model = "RtreemixModel", data = "matrix", ...}{A method for calculating
the GPS values of the data given as 0-1 \code{matrix}.}
\item{model = "RtreemixModel", data = "missing", ...}{A method for calculating
the GPS values of the set of all possible patterns.}
}}

\arguments{
\item{model}{An object of the class \code{RtreemixModel} specifying
the mutagenetic trees mixture model used for deriving the GPS values.
The model should NOT have more than 20 genetic events.}
\item{data}{An \code{RtreemixData} object or a 0-1 \code{matrix}
containing the samples (patterns of genetic events) for which the GPS values
are to be calculated. The length of each of them has to be equal
to the number of genetic events in the \code{model}.}
\item{...}{
\code{sampling.mode} is a \code{character} that specifies the
sampling mode ("constant" or "exponential") used in the waiting time
simulations. Its default value is "exponential".
\code{sampling.param} is a \code{numeric} that specifies the
sampling parameter corresponding to the sampling mode given by
\code{sampling.mode}. Its default value is 1.
\code{no.sim} is an \code{integer} larger than 0 giving the number of
iterations for the waiting time simulations. Its default value is 10.
\code{seed} is a positive \code{integer} specifying the random generator
seed. Its default value is (-1) and then the time is used as a
random generator.
}
}

\value{
The function returns an object from the \code{RtreemixGPS} class that
containes the calculated GPS values, the model used for the
computation, the data, and so on (see
\code{\link{RtreemixGPS-class}}). The GPS values are represented as a
\code{numeric} vector with length equal to the number of samples in \code{data}.
}

\references{Estimating cancer survival and clinical outcome based on
genetic tumor progression scores, J. Rahnenf\"urer et al. }

\note{
The mixture model used for deriving the GPS values should not have more than
20 genetic events. The reason for this is that the number of all possible patterns
for which the GPS values are calculated during a computationally intensive simulations
is in this case 2^20.
The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
For trying out the code please copy it and uncomment it.
}

\author{Jasmina Bogojeska}

\seealso{
\code{\link{RtreemixGPS-class}}, \code{\link{RtreemixData-class}},
\code{\link{RtreemixModel-class}},
\code{\link{fit-methods}}, \code{\link{confIntGPS-methods}}
}

\examples{
## Create an RtreemixData object from a randomly generated RtreemixModel object.
#rand.mod <- generate(K = 2, no.events = 7, noise.tree = TRUE, prob = c(0.2, 0.8))
#data <- sim(model = rand.mod, no.draws = 400)

## Create an RtreemixModel object by fitting model to the given data.
#mod <- fit(data = data, K = 2, equal.edgeweights = TRUE, noise = TRUE)
#show(mod)

## Create an RtreemixGPS object by calculating the GPS for all possible patterns.
#modGPS.all <- gps(model = mod, no.sim = 1000) ## time consuming copmutations
#show(modGPS.all)

## See the GPS values for all possible data.
#GPS(modGPS.all) ## time consuming copmutations

## Create an RtreemixGPS object by calculating the GPS for the data based on the model mod.
#modGPS <- gps(model = mod, data = data, no.sim = 1000)
#show(modGPS) ## time consuming copmutations

## See the GPS values for data.
#GPS(modGPS) ## time consuming copmutations
}


\keyword{methods}
\keyword{survival}


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@30732 bc3139a8-67e5-0310-9ffc-ced21a209358

Jasmina Bogojeska authored on 28/03/2008 15:35:09
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man/gps-methods.Rd
History View file @ 432dbcf
... ... 
@@ -38,7 +38,8 @@
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 \arguments{
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   \item{model}{An object of the class \code{RtreemixModel} specifying
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-    the mutagenetic trees mixture model used for deriving the GPS values.}
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+    the mutagenetic trees mixture model used for deriving the GPS values.
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+    The model should NOT have more than 20 genetic events.}
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   \item{data}{An \code{RtreemixData} object or a 0-1 \code{matrix}
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     containing the samples (patterns of genetic events) for which the GPS values
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     are to be calculated. The length of each of them has to be equal
... ... 
@@ -70,6 +71,10 @@
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   genetic tumor progression scores, J. Rahnenf\"urer et al. }
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 \note{
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+    The mixture model used for deriving the GPS values should not have more than
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+    20 genetic events. The reason for this is that the number of all possible patterns
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+    for which the GPS values are calculated during a computationally intensive simulations
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+    is in this case 2^20.
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     The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
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     For trying out the code please copy it and uncomment it.
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 }
Browse code

added the Rtreemix package and removed the bim package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@28790 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 16/11/2007 21:25:16
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man/gps-methods.Rd
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@@ -0,0 +1,111 @@
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+\name{gps-methods}
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+\docType{methods}
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+
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+\alias{gps}
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+\alias{gps-methods}
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+\alias{gps,RtreemixModel,RtreemixData-method}
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+\alias{gps,RtreemixModel,matrix-method}
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+\alias{gps,RtreemixModel,missing-method}
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+
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+
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+
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+
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+\title{Methods for predicting the GPS of given dataset by
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+  using a given mutagenetic trees mixture model}
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+\description{
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+  These functions compute the genetic progression score (GPS) of each
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+  sample in the given \code{data} by performing a waiting time
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+  simulation along the branchings of the mixture model \code{model}. The
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+  model has to be specified. If a dataset is missing a GPS for all
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+  possible patterns is calculated. The number of events of the samples
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+  in \code{data} equals the number of genetic events in the \code{model}.
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+}
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+
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+\usage{
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+\S4method{gps}{RtreemixModel,RtreemixData}(model, data, ...)
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+\S4method{gps}{RtreemixModel,matrix}(model, data, ...)
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+\S4method{gps}{RtreemixModel,missing}(model, data, ...)
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+}
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+
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+\section{Methods}{\describe{
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+    \item{model = "RtreemixModel", data = "RtreemixData", ...}{A method for calculating
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+      the GPS values of the data given as \code{RtreemixData} object.}
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+    \item{model = "RtreemixModel", data = "matrix", ...}{A method for calculating
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+      the GPS values of the data given as 0-1 \code{matrix}.}
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+    \item{model = "RtreemixModel", data = "missing", ...}{A method for calculating
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+      the GPS values of the set of all possible patterns.}
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+}}
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+
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+\arguments{
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+  \item{model}{An object of the class \code{RtreemixModel} specifying
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+    the mutagenetic trees mixture model used for deriving the GPS values.}
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+  \item{data}{An \code{RtreemixData} object or a 0-1 \code{matrix}
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+    containing the samples (patterns of genetic events) for which the GPS values
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+    are to be calculated. The length of each of them has to be equal
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+    to the number of genetic events in the \code{model}.}
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+  \item{...}{
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+    \code{sampling.mode} is a \code{character} that specifies the
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+    sampling mode ("constant" or "exponential") used in the waiting time
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+    simulations. Its default value is "exponential".
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+    \code{sampling.param} is a \code{numeric} that specifies the
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+    sampling parameter corresponding to the sampling mode given by
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+    \code{sampling.mode}. Its default value is 1.
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+    \code{no.sim} is an \code{integer} larger than 0 giving the number of
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+    iterations for the waiting time simulations. Its default value is 10.
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+    \code{seed} is a positive \code{integer} specifying the random generator
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+    seed. Its default value is (-1) and then the time is used as a
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+    random generator.
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+  }
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+}
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+
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+\value{
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+  The function returns an object from the \code{RtreemixGPS} class that
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+  containes the calculated GPS values, the model used for the
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+  computation, the data, and so on (see
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+  \code{\link{RtreemixGPS-class}}). The GPS values are represented as a
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+  \code{numeric} vector with length equal to the number of samples in \code{data}.
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+}
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+
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+\references{Estimating cancer survival and clinical outcome based on
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+  genetic tumor progression scores, J. Rahnenf\"urer et al. }
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+
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+\note{
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+    The GPS examples are time consuming. They are commented out because of the time restrictions of the check of the package.
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+    For trying out the code please copy it and uncomment it.
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+}
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+
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+\author{Jasmina Bogojeska}
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+
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+\seealso{
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+  \code{\link{RtreemixGPS-class}}, \code{\link{RtreemixData-class}},
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+  \code{\link{RtreemixModel-class}},
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+  \code{\link{fit-methods}}, \code{\link{confIntGPS-methods}}
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+}
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+
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+\examples{
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+## Create an RtreemixData object from a randomly generated RtreemixModel object.
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+#rand.mod <- generate(K = 2, no.events = 7, noise.tree = TRUE, prob = c(0.2, 0.8))
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+#data <- sim(model = rand.mod, no.draws = 400)
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+
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+## Create an RtreemixModel object by fitting model to the given data.
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+#mod <- fit(data = data, K = 2, equal.edgeweights = TRUE, noise = TRUE)
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+#show(mod)
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+
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+## Create an RtreemixGPS object by calculating the GPS for all possible patterns.
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+#modGPS.all <- gps(model = mod, no.sim = 1000) ## time consuming copmutations
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+#show(modGPS.all)
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+
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+## See the GPS values for all possible data.
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+#GPS(modGPS.all) ## time consuming copmutations
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+
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+## Create an RtreemixGPS object by calculating the GPS for the data based on the model mod.
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+#modGPS <- gps(model = mod, data = data, no.sim = 1000)
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+#show(modGPS) ## time consuming copmutations
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+
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+## See the GPS values for data.
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+#GPS(modGPS) ## time consuming copmutations
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+}
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+
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+
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+\keyword{methods}
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+\keyword{survival}