@@ -1,7 +1,7 @@

 Package: NoRCE

 Type: Package

 Title: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

-Version: 1.9.1

+Version: 1.9.2

 Authors@R: c(person("Gulden", "Olgun", 

            email = "gulden@cs.bilkent.edu.tr", 

 		   role = c("aut", "cre")))

@@ -52,8 +52,10 @@

 #'

 #'

 #' @examples

+#' \dontrun{

 #' ncGO<-geneGOEnricher(gene = brain_disorder_ncRNA, org_assembly='hg19',

 #' near=TRUE, genetype = 'Ensembl_gene')

+#' }

 #'

 #' @export

 geneGOEnricher <-

@@ -301,12 +303,13 @@ geneGOEnricher <-

 #' 

 #'

 #' @examples

+#' \dontrun{

 #' #Pathway enrichment based on the gen sets that falls into the TAD regions

 #' ncRNAPathway<-genePathwayEnricher(gene = brain_disorder_ncRNA ,

 #'                                   org_assembly='hg19',

 #'                                   isTADSearch = TRUE,

 #'                                   TAD = tad_hg19,

-#'                                   genetype = 'Ensembl_gene')

+#'                                   genetype = 'Ensembl_gene')}

 #'

 #'

 #' @export

@@ -579,11 +582,12 @@ genePathwayEnricher <-

 #' 

 #' @importFrom rtracklayer import

 #' @examples

-#'

+#' \dontrun{

 #' regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")

 #' regionNC <- rtracklayer::import(regions, format = "BED")

 #' regionGO<-geneRegionGOEnricher(region = regionNC, org_assembly= 'hg19',

 #'                                near = TRUE)

+#'                                }

 #'

 #' @export

 geneRegionGOEnricher <-

@@ -799,12 +803,12 @@ geneRegionGOEnricher <-

 #' @return Pathway enrichment object of the given input

 #'

 #' @examples

-#'

+#' \dontrun{

 #' regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")

 #' regionNC <- rtracklayer::import(regions, format = "BED")

 #' ncPath<-geneRegionPathwayEnricher(region = regionNC,

 #'                                   org_assembly = 'hg19',

-#'                                   near = TRUE)

+#'                                   near = TRUE) }

 #' @export

 geneRegionPathwayEnricher <-

   function(region,

@@ -214,7 +214,7 @@ assembly <- function(org_assembly = c("hg19",

   if (index == 1) {

     mart = useMart(

       biomart = "ENSEMBL_MART_ENSEMBL",

-      host = "grch37.ensembl.org",

+      host = "https://grch37.ensembl.org",

       path = "/biomart/martservice",

       dataset = "hsapiens_gene_ensembl"

     )

@@ -53,12 +53,13 @@ options(readr.num_columns = 0)

 #' @return MiRNA GO term enrichment object for the given input

 #' 

 #' @examples

+#' \dontrun{

 #' subsetGene <- brain_mirna[1:30,]

 #'

 #' miGO <-mirnaGOEnricher(gene=subsetGene,

 #'                        org_assembly='hg19',

 #'                        near = TRUE,

-#'                        target = FALSE)

+#'                        target = FALSE) }

 #' @export mirnaGOEnricher

 mirnaGOEnricher <-

   function(gene,

@@ -22,10 +22,12 @@

 #' @return KEGG pathway enrichment results

 #'

 #' @examples

+#' \dontrun{

 #' subsetGene <- breastmRNA[1:30,]

 #'

 #' br_enr<-KeggEnrichment(genes = subsetGene,

 #'                        org_assembly='hg19')

+#'}

 #'

 #' @export

 #'

@@ -163,7 +165,8 @@ KeggEnrichment <-

 #'

 #'

 #' @examples

-#' br_enr<-reactomeEnrichment(genes = breastmRNA,org_assembly='hg19')

+#' \dontrun{

+#' br_enr<-reactomeEnrichment(genes = breastmRNA,org_assembly='hg19') }

 #'

 #' @export

 reactomeEnrichment <-

@@ -51,9 +51,11 @@ KEGG pathway enrichment results

 KEGG pathway enrichment

 }

 \examples{

+\dontrun{

 subsetGene <- breastmRNA[1:30,]

 br_enr<-KeggEnrichment(genes = subsetGene,

                        org_assembly='hg19')

+}

 }

@@ -97,7 +97,9 @@ Given genes that fall in a given upstream and downstream region of

 mRNAs of interest, GO term enrichment analysis is carried out

 }

 \examples{

+\dontrun{

 ncGO<-geneGOEnricher(gene = brain_disorder_ncRNA, org_assembly='hg19',

 near=TRUE, genetype = 'Ensembl_gene')

+}

 }

@@ -97,12 +97,13 @@ Given genes that fall in the given upstream and downstream region of

 mRNAs of interest, pathway enrichment analysis is carried out

 }

 \examples{

+\dontrun{

 #Pathway enrichment based on the gen sets that falls into the TAD regions

 ncRNAPathway<-genePathwayEnricher(gene = brain_disorder_ncRNA ,

                                   org_assembly='hg19',

                                   isTADSearch = TRUE,

                                   TAD = tad_hg19,

-                                  genetype = 'Ensembl_gene')

+                                  genetype = 'Ensembl_gene')}

 }

@@ -92,10 +92,11 @@ Given gene regions that fall in the given upstream and downstream region

 of mRNAs of interest, GO term enrichment analysis is carried out

 }

 \examples{

-

+\dontrun{

 regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")

 regionNC <- rtracklayer::import(regions, format = "BED")

 regionGO<-geneRegionGOEnricher(region = regionNC, org_assembly= 'hg19',

                                near = TRUE)

+                               }

 }

@@ -92,10 +92,10 @@ Given gene regions that fall in the given upstream and downstream region

 of mRNAs of interest, pathway enrichment analysis is carried out

 }

 \examples{

-

+\dontrun{

 regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")

 regionNC <- rtracklayer::import(regions, format = "BED")

 ncPath<-geneRegionPathwayEnricher(region = regionNC,

                                   org_assembly = 'hg19',

-                                  near = TRUE)

+                                  near = TRUE) }

 }

@@ -96,10 +96,11 @@ GO term enrichments of the microRNA genes with mRNAs that fall in the

 given upstream/downstream regions of the microRNA genes

 }

 \examples{

+\dontrun{

 subsetGene <- brain_mirna[1:30,]

 miGO <-mirnaGOEnricher(gene=subsetGene,

                        org_assembly='hg19',

                        near = TRUE,

-                       target = FALSE)

+                       target = FALSE) }

 }

@@ -51,6 +51,7 @@ Reactome pathway enrichment results

 Reactome pathway enrichment

 }

 \examples{

-br_enr<-reactomeEnrichment(genes = breastmRNA,org_assembly='hg19')

+\dontrun{

+br_enr<-reactomeEnrichment(genes = breastmRNA,org_assembly='hg19') }

 }

@@ -120,7 +120,7 @@ setParameters("searchRegion", "all")

 #Import the gene set regions

 regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")

-regionNC <- import(regions, format = "BED")

+regionNC <- rtracklayer::import(regions, format = "BED")

 #Perform the analysis on the gene regions

 regionGO<-geneRegionGOEnricher(region = regionNC, org_assembly= 'hg19', near = TRUE)

@@ -154,7 +154,7 @@ User-defined TAD regions can be used as an input for the TAD regions and gene en

 ```{r, eval=FALSE}

 # Read the custom TAD boundaries

 cus_TAD<-system.file("extdata", "DER-18_TAD_adultbrain.txt", package = "NoRCE")

-tad_custom <- import(cus_TAD, format = 'bed')

+tad_custom <- rtracklayer::import(cus_TAD, format = 'bed')

 # Use custom TAD boundaries for enrichment

 ncGO_tad <- geneGOEnricher(gene = brain_disorder_ncRNA, org_assembly = 'hg19', genetype = 'Ensembl_gene', isTADSearch = TRUE, TAD = tad_custom)