1. cBioPortalData
  2. man
  3. cBioPortal-class.Rd
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add description for operations method

LiNk-NY authored on 14/01/2025 22:51:24
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 209d3d3
... ... 
@@ -40,7 +40,8 @@ to the functionality provided by the rest of the package.
40 40 
 }
41 41 
 \section{Functions}{
42 42 
 \itemize{
43 
-\item \code{operations(cBioPortal)}:
43 
+\item \code{operations(cBioPortal)}: List all the \code{operations} available with the
44 
+cBioPortal API object, e.g., \code{api$operation}
44 45
45 46 
 }}
46 47 
 \examples{
Browse code

fix typo with Service-class roxygen doc

LiNk-NY authored on 10/12/2024 16:28:09
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 54ed32a
... ... 
@@ -10,7 +10,7 @@
10 10 
 \S4method{operations}{cBioPortal}(x, ..., .deprecated = FALSE)
11 11 
 }
12 12 
 \arguments{
13 
-\item{x}{A \link[=AnVIL:Service-class]{AnVIL} instance or API representation as
13 
+\item{x}{A \link[AnVIL:Services]{AnVIL} instance or API representation as
14 14 
 given by the \link{cBioPortal} function.}
15 15
16 16 
 \item{...}{additional arguments passed to methods or, for
... ... 
@@ -26,14 +26,14 @@ A \code{cBioPortal} class instance
26 26 
 The \code{cBioPortal} class is a representation of the \code{cBioPortal}
27 27 
 API protocol that directly inherits from the \code{Service} class in the
28 28 
 \code{AnVIL} package. For more information, see the
29 
-\link[=AnVIL:Service-class]{AnVIL} package.
29 
+\link[AnVIL:Services]{AnVIL} package.
30 30 
 }
31 31 
 \details{
32 32 
 This class takes the static API as provided at
33 33 
 \url{https://www.cbioportal.org/api/v2/api-docs} and creates an R object
34 34 
 with the help from underlying infrastructure (i.e.,
35 35 
 \link[rapiclient:rapiclient-package]{rapiclient} and
36 
-\link[=AnVIL:Service-class]{AnVIL}) to give the user a unified representation
36 
+\link[AnVIL:Services]{AnVIL}) to give the user a unified representation
37 37 
 of the API specification provided by the cBioPortal group. Users are not
38 38 
 expected to interact with this class other than to use it as input
39 39 
 to the functionality provided by the rest of the package.
... ... 
@@ -49,5 +49,5 @@ cBioPortal()
49 49
50 50 
 }
51 51 
 \seealso{
52 
-\link{cBioPortal}, \link[=AnVIL:Service-class]{AnVIL}
52 
+\link{cBioPortal}, \link[AnVIL:Services]{AnVIL}
53 53 
 }
Browse code

set package anchors in docs

LiNk-NY authored on 09/12/2024 23:01:24
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 711ac1d
... ... 
@@ -10,7 +10,7 @@
10 10 
 \S4method{operations}{cBioPortal}(x, ..., .deprecated = FALSE)
11 11 
 }
12 12 
 \arguments{
13 
-\item{x}{A \linkS4class{Service} instance or API representation as
13 
+\item{x}{A \link[=AnVIL:Service-class]{AnVIL} instance or API representation as
14 14 
 given by the \link{cBioPortal} function.}
15 15
16 16 
 \item{...}{additional arguments passed to methods or, for
... ... 
@@ -26,14 +26,14 @@ A \code{cBioPortal} class instance
26 26 
 The \code{cBioPortal} class is a representation of the \code{cBioPortal}
27 27 
 API protocol that directly inherits from the \code{Service} class in the
28 28 
 \code{AnVIL} package. For more information, see the
29 
-\link[AnVIL:Service]{AnVIL} package.
29 
+\link[=AnVIL:Service-class]{AnVIL} package.
30 30 
 }
31 31 
 \details{
32 32 
 This class takes the static API as provided at
33 33 
 \url{https://www.cbioportal.org/api/v2/api-docs} and creates an R object
34 34 
 with the help from underlying infrastructure (i.e.,
35 35 
 \link[rapiclient:rapiclient-package]{rapiclient} and
36 
-\link[AnVIL:Service]{AnVIL}) to give the user a unified representation
36 
+\link[=AnVIL:Service-class]{AnVIL}) to give the user a unified representation
37 37 
 of the API specification provided by the cBioPortal group. Users are not
38 38 
 expected to interact with this class other than to use it as input
39 39 
 to the functionality provided by the rest of the package.
... ... 
@@ -49,5 +49,5 @@ cBioPortal()
49 49
50 50 
 }
51 51 
 \seealso{
52 
-\link{cBioPortal}, \linkS4class{Service}
52 
+\link{cBioPortal}, \link[=AnVIL:Service-class]{AnVIL}
53 53 
 }
Browse code

fix links in documentation

--as-cran

LiNk-NY authored on 12/01/2024 22:11:12
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 0d85dba
... ... 
@@ -30,7 +30,7 @@ API protocol that directly inherits from the \code{Service} class in the
30 30 
 }
31 31 
 \details{
32 32 
 This class takes the static API as provided at
33 
-\url{https://www.cbioportal.org/api/api-docs} and creates an R object
33 
+\url{https://www.cbioportal.org/api/v2/api-docs} and creates an R object
34 34 
 with the help from underlying infrastructure (i.e.,
35 35 
 \link[rapiclient:rapiclient-package]{rapiclient} and
36 36 
 \link[AnVIL:Service]{AnVIL}) to give the user a unified representation
Browse code

add return value to cBioPortal-class

LiNk-NY authored on 07/10/2022 20:05:00
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 8161d2a
... ... 
@@ -19,6 +19,9 @@ function.}
19 19
20 20 
 \item{.deprecated}{optional logical(1) include deprecated operations?}
21 21 
 }
22 
+\value{
23 
+A \code{cBioPortal} class instance
24 
+}
22 25 
 \description{
23 26 
 The \code{cBioPortal} class is a representation of the \code{cBioPortal}
24 27 
 API protocol that directly inherits from the \code{Service} class in the
Browse code

update docs

LiNk-NY authored on 24/08/2022 14:24:07
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 5ad9d32
... ... 
@@ -14,7 +14,7 @@
14 14 
 given by the \link{cBioPortal} function.}
15 15
16 16 
 \item{...}{additional arguments passed to methods or, for
17 
-`operations,Service-method`, to the internal `get_operation()`
17 
+\verb{operations,Service-method}, to the internal \code{get_operation()}
18 18 
 function.}
19 19
20 20 
 \item{.deprecated}{optional logical(1) include deprecated operations?}
... ... 
@@ -37,9 +37,9 @@ to the functionality provided by the rest of the package.
37 37 
 }
38 38 
 \section{Functions}{
39 39 
 \itemize{
40 
-\item \code{operations,cBioPortal-method}:
41 
-}}
40 
+\item \code{operations(cBioPortal)}:
42 41
42 
+}}
43 43 
 \examples{
44 44
45 45 
 cBioPortal()
Browse code

add cBioPortal-class.R file and move code

LiNk-NY authored on 14/02/2022 23:31:02
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 150c2f1
... ... 
@@ -1,29 +1,50 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/cBioPortal.R
2 
+% Please edit documentation in R/cBioPortal-class.R
3 3 
 \docType{class}
4 4 
 \name{cBioPortal-class}
5 5 
 \alias{cBioPortal-class}
6 6 
 \alias{.cBioPortal}
7 
+\alias{operations,cBioPortal-method}
7 8 
 \title{A class for representing the cBioPortal API protocol}
9 
+\usage{
10 
+\S4method{operations}{cBioPortal}(x, ..., .deprecated = FALSE)
11 
+}
12 
+\arguments{
13 
+\item{x}{A \linkS4class{Service} instance or API representation as
14 
+given by the \link{cBioPortal} function.}
15 
+
16 
+\item{...}{additional arguments passed to methods or, for
17 
+`operations,Service-method`, to the internal `get_operation()`
18 
+function.}
19 
+
20 
+\item{.deprecated}{optional logical(1) include deprecated operations?}
21 
+}
8 22 
 \description{
9 
-The `cBioPortal` class is a representation of the cBioPortal
10 
-    API protocol that directly inherits from the `Service` class in the
11 
-    `AnVIL` package. For more information, see the 'AnVIL' package.
23 
+The \code{cBioPortal} class is a representation of the \code{cBioPortal}
24 
+API protocol that directly inherits from the \code{Service} class in the
25 
+\code{AnVIL} package. For more information, see the
26 
+\link[AnVIL:Service]{AnVIL} package.
12 27 
 }
13 28 
 \details{
14 29 
 This class takes the static API as provided at
15 
-    \url{https://www.cbioportal.org/api/api-docs} and creates an R object
16 
-    with the help from underlying infrastructure (i.e., 'rapiclient' and
17 
-    'AnVIL') to give the user a unified representation of the API
18 
-    specification provided by the cBioPortal group. Users are not
19 
-    expected to interact with this class other than to use it as input
20 
-    to the functionality provided by the rest of the package.
30 
+\url{https://www.cbioportal.org/api/api-docs} and creates an R object
31 
+with the help from underlying infrastructure (i.e.,
32 
+\link[rapiclient:rapiclient-package]{rapiclient} and
33 
+\link[AnVIL:Service]{AnVIL}) to give the user a unified representation
34 
+of the API specification provided by the cBioPortal group. Users are not
35 
+expected to interact with this class other than to use it as input
36 
+to the functionality provided by the rest of the package.
21 37 
 }
38 
+\section{Functions}{
39 
+\itemize{
40 
+\item \code{operations,cBioPortal-method}:
41 
+}}
42 
+
22 43 
 \examples{
23 44
24 45 
 cBioPortal()
25 46
26 47 
 }
27 48 
 \seealso{
28 
-\link{cBioPortal}, \link[AnVIL]{Service}
49 
+\link{cBioPortal}, \linkS4class{Service}
29 50 
 }
Browse code

add details to cBioPortal class doc

LiNk-NY authored on 04/05/2020 21:00:17
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 9c6513f
... ... 
@@ -8,7 +8,16 @@
8 8 
 \description{
9 9 
 The `cBioPortal` class is a representation of the cBioPortal
10 10 
     API protocol that directly inherits from the `Service` class in the
11 
-    `AnVIL` package
11 
+    `AnVIL` package. For more information, see the 'AnVIL' package.
12 
+}
13 
+\details{
14 
+This class takes the static API as provided at
15 
+    \url{https://www.cbioportal.org/api/api-docs} and creates an R object
16 
+    with the help from underlying infrastructure (i.e., 'rapiclient' and
17 
+    'AnVIL') to give the user a unified representation of the API
18 
+    specification provided by the cBioPortal group. Users are not
19 
+    expected to interact with this class other than to use it as input
20 
+    to the functionality provided by the rest of the package.
12 21 
 }
13 22 
 \examples{
14 23
Browse code

rename cbio and update documentation, closes #10

LiNk-NY authored on 16/10/2019 19:25:17
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 94beb5b
... ... 
@@ -4,16 +4,17 @@
4 4 
 \name{cBioPortal-class}
5 5 
 \alias{cBioPortal-class}
6 6 
 \alias{.cBioPortal}
7 
-\title{A class for representing the cBioPortal API}
7 
+\title{A class for representing the cBioPortal API protocol}
8 8 
 \description{
9 
-The cBioPortal class is a product of the cBioPortal API that
10 
-    inherits from the `Service` class
9 
+The `cBioPortal` class is a representation of the cBioPortal
10 
+    API protocol that directly inherits from the `Service` class in the
11 
+    `AnVIL` package
11 12 
 }
12 13 
 \examples{
13 14
14 
-cbio <- cBioPortal()
15 
+cBioPortal()
15 16
16 17 
 }
17 18 
 \seealso{
18 
-AnVIL::Service
19 
+\link{cBioPortal}, \link[AnVIL]{Service}
19 20 
 }
Browse code

make changes for R CMD check

- add documentation for cBioPortal class
- document arguments ..., sampleListId, etc.
- remove .onLoad function (cbioportal) object

LiNk-NY authored on 13/09/2019 18:27:31
Showing 1 changed files
man/cBioPortal-class.Rd
History View file @ 68e6870
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,19 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/cBioPortal.R
3 
+\docType{class}
4 
+\name{cBioPortal-class}
5 
+\alias{cBioPortal-class}
6 
+\alias{.cBioPortal}
7 
+\title{A class for representing the cBioPortal API}
8 
+\description{
9 
+The cBioPortal class is a product of the cBioPortal API that
10 
+    inherits from the `Service` class
11 
+}
12 
+\examples{
13 
+
14 
+cbio <- cBioPortal()
15 
+
16 
+}
17 
+\seealso{
18 
+AnVIL::Service
19 
+}