build: version bump & requirements

quadbio · Mar 1, 2024 · 4c52309 · 4c52309
1 parent 4237466
commit 4c52309
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Showing 2 changed files with 23 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: Pando
-Version: 1.0.5
+Version: 1.1.0
 Type: Package
 Title: Inferring regulomes from multi-modal single-cell genomics data
 Authors@R: person(given = "Jonas Simon",
@@ -20,8 +20,8 @@ Depends:
     R (>= 4.0.0)
 Imports: 
     tidyverse (>= 2.0.0),
-    Seurat (>= 4.0.0),
-    Signac,
+    Seurat (>= 5.0.0),
+    Signac (>= 1.12.0),
     Matrix (>= 1.5-0),
     MatrixGenerics (>= 1.10.0),
     ggplot2,

diff --git a/R/objects.R b/R/objects.R
@@ -105,6 +105,7 @@ RegulatoryNetwork <- setClass(
     )
 )
 
+
 #' The GRNData class
 #'
 #' The GRNData object is an extended \code{Seurat} object
@@ -123,6 +124,7 @@ GRNData <- setClass(
     )
 )
 
+
 #' Get network
 #' @rdname GetNetwork
 #' @method GetNetwork GRNData
@@ -131,6 +133,7 @@ GetNetwork.GRNData <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object@grn, network=network))
 }
 
+
 #' Get network
 #' @rdname GetNetwork
 #' @method GetNetwork RegulatoryNetwork
@@ -154,6 +157,7 @@ NetworkFeatures.GRNData <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@features)
 }
 
+
 #' @rdname NetworkFeatures
 #' @method NetworkFeatures RegulatoryNetwork
 #' @export
@@ -170,6 +174,7 @@ NetworkTFs.GRNData <- function(object){
     return(object@grn@regions@tfs)
 }
 
+
 #' @rdname NetworkTFs
 #' @method NetworkTFs RegulatoryNetwork
 #' @export
@@ -186,6 +191,7 @@ NetworkRegions.GRNData <- function(object){
     return(object@grn@regions)
 }
 
+
 #' @rdname NetworkRegions
 #' @method NetworkRegions RegulatoryNetwork
 #' @export
@@ -211,13 +217,15 @@ NetworkModules.GRNData <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@modules)
 }
 
+
 #' @rdname NetworkModules
 #' @method NetworkModules RegulatoryNetwork
 #' @export
 NetworkModules.RegulatoryNetwork <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@modules)
 }
 
+
 #' @rdname NetworkModules
 #' @method NetworkModules Network
 #' @export
@@ -234,13 +242,15 @@ NetworkParams.GRNData <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@params)
 }
 
+
 #' @rdname NetworkParams
 #' @method NetworkParams RegulatoryNetwork
 #' @export
 NetworkParams.RegulatoryNetwork <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@params)
 }
 
+
 #' @rdname NetworkParams
 #' @method NetworkParams Network
 #' @export
@@ -257,13 +267,15 @@ NetworkGraph.GRNData <- function(object, network=DefaultNetwork(object), graph='
     return(NetworkGraph(GetNetwork(object, network=network), graph=graph))
 }
 
+
 #' @rdname NetworkGraph
 #' @method NetworkGraph RegulatoryNetwork
 #' @export
 NetworkGraph.RegulatoryNetwork <- function(object, network=DefaultNetwork(object), graph='module_graph'){
     return(NetworkGraph(GetNetwork(object, network=network), graph=graph))
 }
 
+
 #' @rdname NetworkGraph
 #' @method NetworkGraph Network
 #' @export
@@ -274,6 +286,7 @@ NetworkGraph.Network <- function(object, graph='module_graph'){
     return(object@graphs[[graph]])
 }
 
+
 #' Get active network
 #' @rdname DefaultNetwork
 #' @method DefaultNetwork GRNData
@@ -282,6 +295,7 @@ DefaultNetwork.GRNData <- function(object){
     return(DefaultNetwork(GetGRN(object)))
 }
 
+
 #' @rdname DefaultNetwork
 #' @method DefaultNetwork RegulatoryNetwork
 #' @export
@@ -298,13 +312,15 @@ coef.GRNData <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@coefs)
 }
 
+
 #' @rdname coef
 #' @method coef RegulatoryNetwork
 #' @export
 coef.RegulatoryNetwork <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@coefs)
 }
 
+
 #' @rdname coef
 #' @method coef Network
 #' @export
@@ -321,13 +337,15 @@ gof.GRNData <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@fit)
 }
 
+
 #' @rdname gof
 #' @method gof RegulatoryNetwork
 #' @export
 gof.RegulatoryNetwork <- function(object, network=DefaultNetwork(object)){
     return(GetNetwork(object, network=network)@fit)
 }
 
+
 #' @rdname gof
 #' @method gof Network
 #' @export
@@ -344,6 +362,7 @@ Params.GRNData <- function(object){
     return(object@grn@params)
 }
 
+
 #' @rdname Params
 #' @method Params RegulatoryNetwork
 #' @export
@@ -397,6 +416,7 @@ LayerData.GRNData <- function(object, ...){
     return(SeuratObject::LayerData(object@data, ...))
 }
 
+
 #' Get variable features from GRNData
 #' @rdname VariableFeatures
 #' @method VariableFeatures GRNData