@@ -511,8 +511,9 @@ loadStudy <- function(

 #'

 #' @description The `cBioDataPack` function allows the user to

 #' download and process cancer study datasets found in MSKCC's cBioPortal.

-#' Output datasets use the \linkS4class{MultiAssayExperiment} data

-#' representation to faciliate analysis and data management operations.

+#' Output datasets use the

+#' [MultiAssayExperiment][MultiAssayExperiment::MultiAssayExperiment-class]

+#' data representation to faciliate analysis and data management operations.

 #'

 #' @details The full list of study identifiers (`studyId`s) can obtained from

 #' `getStudies()`. Currently, only ~ 72% of datasets can be represented as

@@ -536,7 +537,9 @@ loadStudy <- function(

 #' @inheritParams downloadStudy

 #' @inheritParams cBioPortalData

 #'

-#' @return A \linkS4class{MultiAssayExperiment} object

+#' @return A

+#'   [MultiAssayExperiment][MultiAssayExperiment::MultiAssayExperiment-class]

+#'   object

 #'

 #' @seealso <https://www.cbioportal.org/datasets>, [cBioPortalData],

 #'   [removePackCache]

@@ -7,13 +7,13 @@

 #' @description The `cBioPortal` class is a representation of the `cBioPortal`

 #'     API protocol that directly inherits from the `Service` class in the

 #'     `AnVIL` package. For more information, see the

-#'     \link[AnVIL:Service]{AnVIL} package.

+#'     [AnVIL][AnVIL:Service-class] package.

 #'

 #' @details This class takes the static API as provided at

 #'     <https://www.cbioportal.org/api/v2/api-docs> and creates an R object

 #'     with the help from underlying infrastructure (i.e.,

-#'     \link[rapiclient:rapiclient-package]{rapiclient} and

-#'     \link[AnVIL:Service]{AnVIL}) to give the user a unified representation

+#'     [rapiclient][rapiclient::rapiclient-package] and

+#'     [AnVIL][AnVIL:Service-class]) to give the user a unified representation

 #'     of the API specification provided by the cBioPortal group. Users are not

 #'     expected to interact with this class other than to use it as input

 #'     to the functionality provided by the rest of the package.

@@ -22,7 +22,7 @@

 #'

 #' @return A `cBioPortal` class instance

 #'

-#' @seealso  [cBioPortal], \linkS4class{Service}

+#' @seealso  [cBioPortal], [AnVIL][AnVIL:Service-class]

 #'

 #' @examples

 #'

@@ -40,7 +40,7 @@

 #' @importFrom AnVIL operations

 #' @importFrom methods callNextMethod

 #'

-#' @param x A \linkS4class{Service} instance or API representation as

+#' @param x A [AnVIL][AnVIL:Service-class] instance or API representation as

 #'     given by the [cBioPortal] function.

 #'

 #' @inheritParams AnVIL::operations

@@ -226,7 +226,9 @@ update.args <- function(args) {

 #'         c("acc_tcga_rppa", "acc_tcga_linear_CNA", "acc_tcga_mutations")

 #' )

 #'

-#' @return A \linkS4class{MultiAssayExperiment} object

+#' @return A

+#'   [MultiAssayExperiment][MultiAssayExperiment::MultiAssayExperiment-class]

+#'   object

 #'

 #' @seealso [cBioDataPack], [removeDataCache]

 #'

@@ -45,13 +45,16 @@ to be created when using \code{downloadStudy}.}

 'pedcbioportal.kidsfirstdrc.org'}

 }

 \value{

-A \linkS4class{MultiAssayExperiment} object

+A

+\link[MultiAssayExperiment:MultiAssayExperiment-class]{MultiAssayExperiment}

+object

 }

 \description{

 The \code{cBioDataPack} function allows the user to

 download and process cancer study datasets found in MSKCC's cBioPortal.

-Output datasets use the \linkS4class{MultiAssayExperiment} data

-representation to faciliate analysis and data management operations.

+Output datasets use the

+\link[MultiAssayExperiment:MultiAssayExperiment-class]{MultiAssayExperiment}

+data representation to faciliate analysis and data management operations.

 }

 \details{

 The full list of study identifiers (\code{studyId}s) can obtained from

@@ -10,7 +10,7 @@

 \S4method{operations}{cBioPortal}(x, ..., .deprecated = FALSE)

 }

 \arguments{

-\item{x}{A \linkS4class{Service} instance or API representation as

+\item{x}{A \link[=AnVIL:Service-class]{AnVIL} instance or API representation as

 given by the \link{cBioPortal} function.}

 \item{...}{additional arguments passed to methods or, for

@@ -26,14 +26,14 @@ A \code{cBioPortal} class instance

 The \code{cBioPortal} class is a representation of the \code{cBioPortal}

 API protocol that directly inherits from the \code{Service} class in the

 \code{AnVIL} package. For more information, see the

-\link[AnVIL:Service]{AnVIL} package.

+\link[=AnVIL:Service-class]{AnVIL} package.

 }

 \details{

 This class takes the static API as provided at

 \url{https://www.cbioportal.org/api/v2/api-docs} and creates an R object

 with the help from underlying infrastructure (i.e.,

 \link[rapiclient:rapiclient-package]{rapiclient} and

-\link[AnVIL:Service]{AnVIL}) to give the user a unified representation

+\link[=AnVIL:Service-class]{AnVIL}) to give the user a unified representation

 of the API specification provided by the cBioPortal group. Users are not

 expected to interact with this class other than to use it as input

 to the functionality provided by the rest of the package.

@@ -49,5 +49,5 @@ cBioPortal()

 }

 \seealso{

-\link{cBioPortal}, \linkS4class{Service}

+\link{cBioPortal}, \link[=AnVIL:Service-class]{AnVIL}

 }

@@ -55,7 +55,9 @@ non-interactive session, data download will be attempted; equivalent to

 to be created when using \code{downloadStudy}.}

 }

 \value{

-A \linkS4class{MultiAssayExperiment} object

+A

+\link[MultiAssayExperiment:MultiAssayExperiment-class]{MultiAssayExperiment}

+object

 }

 \description{

 Obtain a \code{MultiAssayExperiment} object for a particular gene panel,

@@ -103,5 +103,6 @@ loadStudy(file_dir)

 }

 \seealso{

-\link{cBioDataPack}, \linkS4class{MultiAssayExperiment}

+\link{cBioDataPack},

+\link[MultiAssayExperiment:MultiAssayExperiment-class]{MultiAssayExperiment}

 }