migrate to v5

melsiddieg · Nov 23, 2023 · 0c5400a · 0c5400a
1 parent 57570be
commit 0c5400a
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Showing 11 changed files with 26 additions and 243 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,12 +23,25 @@ biocViews: Annotation, VariantAnnotation
 Lazy: TRUE
 LazyData: TRUE
 Encoding: UTF-8
-Collate: 'commons.R' 'AllClasses.R' 'AllGenerics.R'
-        'AnnotateVcf-methods.R' 'CellBaseParam-methods.R'
-        'CellBaseR-methods.R' 'cellbase.R' 'getCellbase-methods.R'
-        'getChromosomeInfo-methods.R' 'getClinical-methods.R'
-        'getGene-methods.R' 'getMeta-methods.R' 'getProtein-methods.R'
-        'getRegion-methods.R' 'getSnp-methods.R' 'getTf-methods.R'
-        'getTranscript-methods.R' 'getVariant-methods.R'
-        'getXref-methods.R' 'show-methods.R' 'tools.R' 'user.R'
+Collate: 
+    'commons.R'
+    'AllClasses.R'
+    'AllGenerics.R'
+    'AnnotateVcf-methods.R'
+    'CellBaseParam-methods.R'
+    'CellBaseR-methods.R'
+    'cellbase.R'
+    'getCellbase-methods.R'
+    'getChromosomeInfo-methods.R'
+    'getClinical-methods.R'
+    'getGene-methods.R'
+    'getMeta-methods.R'
+    'getProtein-methods.R'
+    'getRegion-methods.R'
+    'getTranscript-methods.R'
+    'getVariant-methods.R'
+    'getXref-methods.R'
+    'show-methods.R'
+    'tools.R'
+    'user.R'
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,7 +8,6 @@ export(getConservationByRegion)
 export(getGeneInfo)
 export(getProteinInfo)
 export(getRegulatoryByRegion)
-export(getSnpByGene)
 export(getTranscriptByGene)
 export(getVariantAnnotation)
 exportClasses(CellBaseParam)
@@ -21,8 +20,6 @@ exportMethods(getGene)
 exportMethods(getMeta)
 exportMethods(getProtein)
 exportMethods(getRegion)
-exportMethods(getSnp)
-exportMethods(getTf)
 exportMethods(getTranscript)
 exportMethods(getVariant)
 exportMethods(getXref)

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -18,8 +18,6 @@ standardGeneric("getRegion"))
 ###############################################################################
 
 ###############################################################################
-setGeneric("getSnp", function(object,ids,resource,param=NULL)
-standardGeneric("getSnp"))
 
 ###############################################################################
 
@@ -35,9 +33,7 @@ standardGeneric("getCellBase"))
 
 ###############################################################################
 
-###############################################################################
-setGeneric("getTf", function(object,ids,resource,param=NULL)
-standardGeneric("getTf"))
+
 
 ###############################################################################
 

diff --git a/R/getMeta-methods.R b/R/getMeta-methods.R
@@ -29,7 +29,7 @@ setMethod("getMeta", "CellBaseR",    definition = function(object, resource){
     result <- fetchCellbase(object=object, file=NULL, meta=meta, categ=categ,
                             subcateg=subcateg,
                             ids=ids, resource=resource, param=NULL)
-    data <- lapply(result, function(x)as.data.frame(x))
-    result <- rbind_pages(data)
-    return(result)
+    #data <- lapply(result, function(x)as.data.frame(x))
+    #result <- rbind_pages(data)
+    return(result[,c(1:4)])
 })
diff --git a/R/getSnp-methods.R b/R/getSnp-methods.R
diff --git a/R/getTf-methods.R b/R/getTf-methods.R
diff --git a/R/user.R b/R/user.R
@@ -35,24 +35,7 @@ getGeneInfo <- function(object, id, param=NULL){
                  param = param)
   res
 }
-##############################################################################
-#' getSnpByGene
-#' 
-#' A convienice method to fetch known variants (snps) for specific gene/s
-#' @param object an object of class CellBaseR
-#' @param id a charcter vector of HUGO symbol (gene names)
-#' @param param an object of class CellBaseParam
-#' @return a dataframe of the query result
-#' @examples 
-#' cb <- CellBaseR()
-#' param <- CellBaseParam(limit = 10)
-#' res <- getSnpByGene(cb, "TET1", param = param)
-#' @export
-getSnpByGene <- function(object, id, param=NULL){
-
-  res <- getGene(object = object, ids = id, resource = "snp", param = param)
-  res
-}
+
 ##############################################################################
 #' getProteinInfo
 #' 

diff --git a/man/getSnp-CellBaseR-method.Rd b/man/getSnp-CellBaseR-method.Rd
diff --git a/man/getSnpByGene.Rd b/man/getSnpByGene.Rd
diff --git a/man/getTf-CellBaseR-method.Rd b/man/getTf-CellBaseR-method.Rd
diff --git a/vignettes/cellbaseR.Rmd b/vignettes/cellbaseR.Rmd
@@ -39,7 +39,6 @@ The cellbaseR package
 provide many methods to query the cellbase webservices, they include:  
 
 -  getGene  
--  getSnp 
 -  getProtein   
 -  getTranscript
 -  getRegion 
@@ -116,7 +115,6 @@ queries. These include:
 - getClinicalByGene
 - getTranscriptByGene
 - getGeneInfo
-- getSnpByGene
 - getProteinInfo
 - getClinicalByRegion
 - getConservationByRegion