@@ -1,20 +1,20 @@

 Package: NoRCE

 Type: Package

 Title: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

-Version: 1.9.0

+Version: 1.9.1

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

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

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

 Description: While some non-coding RNAs (ncRNAs) are assigned  critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint to a functional association. We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast.

 License: MIT + file LICENSE

-Depends: R (>= 4.0) 

+Depends: R (>= 4.2.0) 

 Imports:

-  KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,

+  KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,

   S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl,

   dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc,

   biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi

 Encoding: UTF-8

-RoxygenNote: 7.1.1

+RoxygenNote: 7.2.1

 Suggests: 

     knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene,

     TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene,

@@ -40,6 +40,7 @@ import(GO.db)

 import(GenomicFeatures)

 import(dbplyr)

 import(readr)

+import(stringr)

 import(zlibbioc)

 importFrom(AnnotationDbi,Term)

 importFrom(AnnotationDbi,mappedkeys)

@@ -89,18 +89,22 @@ goEnrichment <-

            enrichTest = c("hyper", "binom", "fisher", "chi")) {

     if (missing(org_assembly)) {

       message("Genome assembly version is missing.")

-      assembly(org_assembly)

     }

     if (missing(genes)) {

       message("Genes are missing. Expected input: FOXP2 SOX4 HOXC6")

     }

+    assembly(org_assembly)

     #  annot <- unique(annGO(genes, GOtype, org_assembly))

     goData <- annGO(genes, GOtype, org_assembly)

     annot <- goData[[2]]

     uniqueGO <- annot$GOID[!duplicated(annot$GOID)]

-    

-    gofreq <- as.data.frame(table(annot$GOID))

+    if(is.null(dim(backG)[1])){

+      gofreq <- as.data.frame(table(annot$GOID))

+    }else{

+      

+    }

+   

     notGene <-

       getBackGenes(

         backgroundGene = backG,

@@ -118,45 +122,25 @@ goEnrichment <-

     freq <- merge(gofreq, notGene, by = "Var1")

     found <- freq$Freq.x

-    ifelse(backG == '',

+    ifelse(is.null(dim(backG)[1]),

            geneSize <- length(unique(goData[[1]]$Gene)),

-           geneSize <- length(unique(backG)))

-    

+           geneSize <- dim(unique(backG))[1])

     M <- freq$Freq.y

     n <- rep(length(unique(annot$Gene)), length(M))

-    

-    #  if (enrichTest == "binom") {

-    #    pvalues <- 2 * (1 - pbinom(found, n, pCut))

-    #  }

-    # if (enrichTest == "fisher") {

-    #    pvalues <-

-    #     fisher.test(matrix(c(

-    #      found, (M - found), (n - found), (geneSize - M - n + found)

-    #        ), 2, 2), alternative = 'greater')$p.value

-    #   }

-    #  if (enrichTest == "chi") {

-    #   pvalues <-

-    #    chisq.test(matrix(c(

-    #     found, (M - found), (n - found), (geneSize - M - n + found)

-    #  )))$p.value

-    #    }

-    #   else {

-    #    pvalues <- phyper(found - 1, M, geneSize - M, n, lower.tail = FALSE)

-    # }

     ifelse(

-      enrichTest == "binom",

+      pkg.env$enrichTest == "binom",

       pvalues <-

         2 * (1 - pbinom(found, n, pCut)),

       ifelse(

-        enrichTest == "fisher",

+        pkg.env$enrichTest == "fisher",

         pvalues <-

           fisher.test(matrix(c(

             found, (M - found), (n - found), (geneSize - M - n + found)

           ), 2, 2), alternative = 'greater')$p.value,

         ifelse(

-          enrichTest == "chi",

+          pkg.env$enrichTest == "chi",

           pvalues <-

             chisq.test(matrix(c(

               found, (M - found), (n - found), (geneSize - M - n + found)

@@ -229,12 +213,12 @@ getBackGenes <-

                             "dm6",

                             "ce11",

                             "sc3"),

-           type = 'pc_gene') {

-    if (backgroundGene == '') {

+           type = c('pc_gene', 'mirna')) {

+    backgroundGene = as.data.frame(backgroundGene)

+    if (length(backgroundGene[,1]) == 1) {

       bckfreq <- as.data.frame(table(all$GOID))

     }

     else{

-      backgroundGene = as.data.frame(backgroundGene)

       colnames(backgroundGene) = 'bg'

       if (type == 'mirna') {

@@ -252,13 +236,12 @@ getBackGenes <-

           getUCSC(geneTargetLoc, 10000, 10000, org_assembly)

         colnames(backgroundGene) = 'bg'

       }

-      annot <-

-        unique(annGO(backgroundGene$bg, GOtype, org_assembly))

-      uniqueGO <- annot$GOID[!duplicated(annot$GOID)]

+      goData <-annGO(backgroundGene$bg, GOtype, org_assembly)

+      annot <- goData[[2]]

       bckfreq <- as.data.frame(table(annot$GOID))

     }

     bb <- bckfreq[bckfreq$Var1 %in% gofreq$Var1,]

     return(bb)

-  }

+  }

\ No newline at end of file

@@ -14,6 +14,7 @@

 #' @return Data frame of the miRNA-mRNA correlation result

 #' 

 #' @import dbplyr

+#' @import stringr

 #'

 #' @export

 corrbased <- function(mirnagene,

@@ -22,29 +23,20 @@ corrbased <- function(mirnagene,

                       databaseFile) {

   colnames(mirnagene) <- c('g')

-  conn <- DBI::dbConnect(RSQLite::SQLite(), databaseFile)

-  

   a <-

     as.data.frame(gsub(paste(c("-3p", "-5p"), collapse = "|"), "",

                        mirnagene$g))

-  colnames(a) <- 'genes'

-  a <- unique(rbind(a, mirnagene$g))

+  a <- data.frame(str_replace_all(a[,1], 'miR', 'mir'))

+  colnames(a) <- 'g'

+  a <- unique(rbind(a, mirnagene))

-  # dat <-

-  #   cRegulome::get_mir(

-  #     conn = conn,

-  #     mir = as.character(a$genes),

-  #     study = cancer,

-  #     min_abs_cor = minAbsCor

-  #   )

-  # colnames(dat) <- c("mirna_base", "feature", "cor", "cancer")

-

+  conn <- DBI::dbConnect(RSQLite::SQLite(), databaseFile)

   dat <- conn %>%

     dplyr::tbl('cor_mir') %>%

     dplyr::select(mirna_base, feature, cancer) %>%

-    dplyr::filter(mirna_base %in% local(mirnagene$g)) %>%

+    dplyr::filter(mirna_base %in% local(a$g)) %>%

     dplyr::collect() %>%

     tidyr::gather(cancer, cor, -mirna_base, -feature) %>%

     dplyr::mutate(cor = cor / 100) %>% dplyr::filter(abs(cor) > minAbsCor) %>%

@@ -93,24 +85,34 @@ corrbasedMrna <-

 #' Get TCGA miRNAseq expression of miRNA genes for the given cancer

 #'

 #' @param mirnagene Data frame of the mature format

-#' @param cancer Name of the TCGA project code such as 'BRCA' that is

-#'      analyzed for miRNA-mRNA correlation

+#' @param cancer Name of the TCGA project code such as 'BRCA'

 #' @param databaseFile Path of miRcancer.db file

 #'

 #' @return Data frame of the raw read count of the given miRNA genes

 #'       for different patients

+#'       

+#' @import dbplyr

+#' @import stringr

 #'

 #' @export

 getmiRNACount <- function(mirnagene, cancer, databaseFile) {

   colnames(mirnagene) <- c('g')

+  a <-

+    as.data.frame(gsub(paste(c("-3p", "-5p"), collapse = "|"), "",

+                       mirnagene$g))

+  

+  a <- data.frame(str_replace_all(a[,1], 'miR', 'mir'))

+  colnames(a) <- 'g'

+  a <- unique(rbind(a, mirnagene))

+  

   conn <- DBI::dbConnect(RSQLite::SQLite(), databaseFile)

   dat <-

     conn %>%

     dplyr::tbl('profiles') %>%

     dplyr::select(study, mirna_base, count) %>%

-    dplyr::filter(mirna_base %in% !!mirnagene$g) %>%

+    dplyr::filter(mirna_base %in% !!a$g) %>%

     dplyr::filter(study %in% cancer) %>%

     dplyr::collect() %>% na.omit()

@@ -98,9 +98,8 @@ geneGOEnricher <-

     if (missing(genetype))

       message("Input gene type is missing.")

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    assembly(org_assembly)

+    

     gene <- as.data.frame(gene)

     colnames(gene) <- c("genes")

     geneLoc <-

@@ -350,9 +349,8 @@ genePathwayEnricher <-

     if (missing(org_assembly)) {

       message("Assembly version is missing?")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    assembly(org_assembly)

+    

     if (missing(genetype))

       message("Input gene type is missing.")

@@ -619,9 +617,7 @@ geneRegionGOEnricher <-

     if (missing(org_assembly)) {

       message("Assembly version is missing?")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    assembly(org_assembly)

     if (near) {

       ifelse(

         pkg.env$searchRegion == 'all',

@@ -738,7 +734,16 @@ geneRegionGOEnricher <-

           pAdjust = pkg.env$pAdjust,

           min = pkg.env$min

         )

-      

+      if (length(enrichedGene@Term) > 0)

+      {

+        enrichedGene@ncGeneList <- commonGeneRegion(

+          mrnaobject = enrichedGene,

+          org_assembly = org_assembly,

+          downstream = pkg.env$downstream,

+          upstream = pkg.env$upstream,

+          inRegion =  region

+        )

+      }

       return(enrichedGene)

     }

@@ -832,9 +837,9 @@ geneRegionPathwayEnricher <-

     if (missing(org_assembly)) {

       message("Assembly version is missing?")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    

+    assembly(org_assembly)

+    

     if (near) {

       ifelse(

@@ -277,9 +277,7 @@ getUCSC <-

                             "dm6",

                             "ce11",

                             "sc3")) {

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    

     if (missing(bedfile)) {

       message("Bed file is missing?")

     }

@@ -293,6 +291,8 @@ getUCSC <-

       message("genomee assembly version is missing.")

     }

+    assembly(org_assembly)

+    

     big_islands <-

       resize(bedfile, width = downstream + width(bedfile), fix = "end")

     rt1 <-

@@ -345,18 +345,19 @@ getNearToExon <-

                             "dm6",

                             "ce11",

                             "sc3")) {

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

     if (missing(bedfile)) {

       message("Bed file is missing?")

     }

+    if (missing(org_assembly)) {

+      message("Assembly is missing?")

+    }

     if (missing(upstream)) {

       message("Upstream information is missing?")

     }

     if (missing(downstream)) {

       message("Downstream information is missing?")

     }

+    assembly(org_assembly)

     big_islands <-

       resize(bedfile, width = downstream + width(bedfile), fix = "end")

@@ -412,9 +413,8 @@ getNearToIntron <-

     if (missing(org_assembly)) {

       message("Assembly is missing?")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    assembly(org_assembly)

+    

     if (missing(bedfile)) {

       message("Bed file is missing?")

     }

@@ -496,9 +496,9 @@ getTADOverlap <-

     if (missing(org_assembly)) {

       message("Assembly is missing?")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    

+    assembly(org_assembly)

+    

     if (missing(bedfile)) {

       message("Bed file is missing?")

     }

@@ -576,7 +576,7 @@ convertGeneID <-

                             "ce11",

                             "sc3")) {

     if (missing(org_assembly)) {

-      message("genomee assembly version is missing.")

+      message("Genome assembly version is missing.")

     }

     if (missing(genetype)) {

       message("Format of the gene is missing.")

@@ -584,9 +584,9 @@ convertGeneID <-

     if (missing(genelist)) {

       message("List of gene is missing.")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    

+    assembly(org_assembly)

+    

     attributes <-

       c("chromosome_name",

         "start_position",

@@ -630,31 +630,30 @@ convertGeneID <-

                 mart = pkg.env$mart

               ),

             ifelse(

-              genetype == "NCBI",

+              (genetype == "NCBI" & (org_assembly == 'hg19' | org_assembly == 'hg38')),

               output <-

                 getBM(

                   attributes = c("hgnc_symbol", attributes),

                   filters = "hgnc_symbol",

                   values = genelist,

-                  mart = pkg.env$mart,

-                  ifelse(

-                    genetype == "mgi_symbol",

-                    output <-

-                      getBM(

-                        attributes = c("mgi_symbol", attributes),

-                        filters = "mgi_symbol",

-                        values = genelist,

-                        mart = pkg.env$mart

-                      ),

-                    output <-

-                      getBM(

-                        attributes = c("external_gene_name", attributes),

-                        filters = "external_gene_name",

-                        values = genelist,

-                        mart = pkg.env$mart

-                      )

+                  mart = pkg.env$mart),

+              ifelse(

+                (genetype == "NCBI" & org_assembly == 'mm10'),

+                output <-

+                  getBM(

+                    attributes = c("mgi_symbol", attributes),

+                    filters = "mgi_symbol",

+                    values = genelist,

+                    mart = pkg.env$mart

+                  ),

+                output <-

+                  getBM(

+                    attributes = c("external_gene_name", attributes),

+                    filters = "external_gene_name",

+                    values = genelist,

+                    mart = pkg.env$mart

                   )

-                )

+              )

             )

           )

         )

@@ -96,9 +96,9 @@ mirnaGOEnricher <-

         !is.character(gene) & !is.factor(gene))

       message("Type of the gene should be data.frame or character")

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    

+    assembly(org_assembly)

+    

     gene <- as.data.frame(gene)

     colnames(gene) <- c("genes")

@@ -380,9 +380,9 @@ mirnaPathwayEnricher <-

     if (missing(org_assembly)) {

       message("Assembly version is missing.")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    

+    assembly(org_assembly)

+    

     if (!is.data.frame(gene) &

         !is.character(gene) & !is.factor(gene))

@@ -692,9 +692,9 @@ mirnaRegionGOEnricher <-

     if (missing(org_assembly)) {

       message("Assembly version is missing.")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    

+    assembly(org_assembly)

+    

     if (target) {

       genes <-

@@ -863,6 +863,16 @@ mirnaRegionGOEnricher <-

           min = pkg.env$min,

           enrichTest = pkg.env$enrichTest

         )

+      if (length(miEnrich@Term) > 0)

+      {

+        miEnrich@ncGeneList <- commonGeneRegion(

+          mrnaobject = miEnrich,

+          org_assembly = org_assembly,

+          downstream = pkg.env$downstream,

+          upstream = pkg.env$upstream,

+          inRegion =  region

+        )

+      }

       return(miEnrich)

     }

@@ -961,9 +971,8 @@ mirnaRegionPathwayEnricher <-

       message("Assembly version is missing.")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    assembly(org_assembly)

+    

     if (target) {

       genes <-

@@ -1210,14 +1219,14 @@ predictmiTargets <- function(gene, type, org_assembly)

     ifelse(

       org_assembly == 'mm10',

       targets <- read.table(paste0("https://raw.githubusercontent.com/",

-              "guldenolgun/NoRCE-data/master/target/target_mouse.txt")),

+                                   "guldenolgun/NoRCE-data/master/target/target_mouse.txt")),

       ifelse(

         org_assembly == 'dre10',

         markk <- 2,

         ifelse (

           org_assembly == 'ce11',

           targets <- read.table(paste0("https://raw.githubusercontent.com/",

-                "guldenolgun/NoRCE-data/master/target/target_worm.txt")),

+                                       "guldenolgun/NoRCE-data/master/target/target_worm.txt")),

           ifelse (

             org_assembly == 'rn6',

             markk <- 1,

@@ -1225,10 +1234,10 @@ predictmiTargets <- function(gene, type, org_assembly)

               org_assembly == 'dm6',

               targets <- read.table(paste0(

                 "https://raw.githubusercontent.com/",

-                    "guldenolgun/NoRCE-data/master/target/target_fly.txt"),

-                      skip = 1),

-            targets <- read.table(paste0("https://raw.githubusercontent.com/",

-                    "guldenolgun/NoRCE-data/master/target/target_human.txt"))

+                "guldenolgun/NoRCE-data/master/target/target_fly.txt"),

+                skip = 1),

+              targets <- read.table(paste0("https://raw.githubusercontent.com/",

+                                           "guldenolgun/NoRCE-data/master/target/target_human.txt"))

             )

           )

         )

@@ -1239,13 +1248,13 @@ predictmiTargets <- function(gene, type, org_assembly)

   if(markk == 1){

     tmp1 <- read.table(paste0("https://raw.githubusercontent.com/",

-                "guldenolgun/NoRCE-data/master/target/target_rat.txt"))

+                              "guldenolgun/NoRCE-data/master/target/target_rat.txt"))

     tmp2 <- read.table(paste0("https://raw.githubusercontent.com/",

-                "guldenolgun/NoRCE-data/master/target/target_rat1.txt"))

+                              "guldenolgun/NoRCE-data/master/target/target_rat1.txt"))

     tmp3 <- read.table(paste0("https://raw.githubusercontent.com/",

-                "guldenolgun/NoRCE-data/master/target/target_rat2.txt"))

+                              "guldenolgun/NoRCE-data/master/target/target_rat2.txt"))

     tmp4 <- read.table(paste0("https://raw.githubusercontent.com/",

-                "guldenolgun/NoRCE-data/master/target/target_rat3.txt"))

+                              "guldenolgun/NoRCE-data/master/target/target_rat3.txt"))

     target <- rbind(tmp1,tmp2,tmp3)

     targets <- merge(target,tmp4, by = 'V1')

     colnames(targets) <- c("ens","mir","sym","trans")

@@ -1253,9 +1262,9 @@ predictmiTargets <- function(gene, type, org_assembly)

   if(markk  == 2){

     tmp1 <- read.table(paste0("https://raw.githubusercontent.com/",

-                "guldenolgun/NoRCE-data/master/target/target_zebra.txt"))

+                              "guldenolgun/NoRCE-data/master/target/target_zebra.txt"))

     tmp2 <- read.table(paste0("https://raw.githubusercontent.com/",

-                "guldenolgun/NoRCE-data/master/target/target_zebra1.txt"))

+                              "guldenolgun/NoRCE-data/master/target/target_zebra1.txt"))

     targets <- cbind(rbind(tmp1,tmp2),"")

     colnames(target) <- c("ens","sym","mir","trans")

   }

@@ -1265,16 +1274,16 @@ predictmiTargets <- function(gene, type, org_assembly)

   ifelse(type == "NCBI",

          where <-

-           targets[which(tolower(targets$sym) %in% gene$genes),],

+           targets[which(tolower(targets$sym) %in% tolower(gene$genes)),],

          ifelse (

            type == "mirna",

            where <-

              targets[which(tolower(targets$mir) %in% tolower(gene$genes)),],

            ifelse (type == "Ensembl_gene" ,

                    where <-

-                     targets[which(tolower(targets$ens) %in% gene$genes),],

+                     targets[which(tolower(targets$ens) %in% tolower(gene$genes)),],

                    where <-

-                     targets[which(tolower(targets$trans) %in% gene$genes),])

+                     targets[which(tolower(targets$trans) %in% tolower(gene$genes)),])

          ))

   if (nrow(where) == 0) {

     return(NULL)

@@ -59,9 +59,8 @@ KeggEnrichment <-

     if (missing(org_assembly)) {

       message("Assembly version is missing.")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

       assembly(org_assembly)

-    }

+    

     pathTable <- unique(keggPathwayDB(org_assembly))

     genes <- as.data.frame(genes)

     colnames(genes) <- 'g'

@@ -197,9 +196,9 @@ reactomeEnrichment <-

     if (missing(org_assembly)) {

       message("Assembly version is missing.")

     }

-    if (class(pkg.env$mart)[1] != "Mart") {

+

       assembly(org_assembly)

-    }

+    

     pathTable <- unique(reactomePathwayDB(org_assembly))

     genes <- as.data.frame(genes)

     colnames(genes) <- 'g'

@@ -659,10 +658,9 @@ pathwayEnrichment <- function(genes,

   if (missing(isSymbol))

     message("GMT gene format is missing.")

-  

-  if (class(pkg.env$mart)[1] != "Mart") {

+

     assembly(org_assembly)

-  }

+  

   genes <- as.data.frame(genes)

   colnames(genes) <- 'g'

@@ -24,7 +24,6 @@ drawDotPlot <- function(mrnaObject, type = "pAdjust", n) {

   tmp <- topEnrichment(mrnaObject, type, n)

   if (type == "pvalue") {

     p <-

-      p <-

       ggplot(tmp, aes(x = Pvalue, y = reorder(Term, Pvalue))) +

       geom_point(aes(size = EnrichGeneNumber, color =

                        Pvalue), position = "dodge") + theme_bw() + theme(

@@ -39,7 +38,7 @@ drawDotPlot <- function(mrnaObject, type = "pAdjust", n) {

                        ) + labs(

                          x =

                            "p-value",

-                         y = "GO Terms",

+                         y = "Terms",

                          color = "p-value",

                          size = "Gene Count"

                        )

@@ -60,7 +59,7 @@ drawDotPlot <- function(mrnaObject, type = "pAdjust", n) {

                        ) + labs(

                          x =

                            "pAdjust-value",

-                         y = "GO Terms",

+                         y = "Terms",

                          color = "p-Adj",

                          size = "Gene Count"

                        )

@@ -124,6 +123,12 @@ writeEnrichment <-

 #' @return Give top n enrichment results

 #' 

 #' @importFrom dplyr %>%

+#' 

+#' @examples 

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

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

+#'    

+#' result = topEnrichment(mrnaObject = ncGO, type = "pvalue", n = 10)

 #'

 #' @export

 topEnrichment <- function(mrnaObject, type, n) {

@@ -145,11 +150,13 @@ topEnrichment <- function(mrnaObject, type, n) {

   ),

   go = unlist(mrnaObject@geneList))

+  tmp <- mrnaObject@ncGeneList

+  is.na(tmp) <- lengths(tmp) == 0

   table1 <- data.frame(gene = rep(

     names(mrnaObject@geneList),

-    lapply(mrnaObject@ncGeneList, length)

+    lapply(tmp, length)

   ),

-  go = unlist(mrnaObject@ncGeneList))

+  go = unlist(tmp))

   table <- table[!duplicated(table), ]

@@ -357,7 +364,7 @@ createNetwork <-

         layout = l * 1.0

       )

     return(p)

-    }

+  }

 #' Plot and save the GO term DAG of the top n enrichments in terms of 

 #' p-values or adjusted p-values with an user provided format

@@ -414,7 +421,7 @@ getGoDag <-

     node_color <-

       grDevices::colorRampPalette(c("lightgoldenrodyellow", "orangered"),

-                       bias = 0.5)(length(p_range))

+                                  bias = 0.5)(length(p_range))

     color <- seq_along(dt$Pvalue)#seq_len(2)

     if (type == 'pvalue') {

@@ -499,9 +506,7 @@ getKeggDiagram <-

     if (missing(pathway))

       message("Expected pathway ID is missing. Please specify pathway ID")

-    if (class(pkg.env$mart)[1] != "Mart") {

-      assembly(org_assembly)

-    }

+    assembly(org_assembly)

     path_index <- which(names(mrnaObject@geneList) == pathway)

     ns <- unique(

@@ -514,15 +519,15 @@ getKeggDiagram <-

     )

     n <- paste(ns$entrezgene_id, collapse = '/')

     if(identical(interactive(), TRUE)){

-    browseURL(

-      paste0(

-        "http://www.kegg.jp/kegg-bin/show_pathway?",

-        pathway,

-        '/',

-        n,

-        collapse = ''

+      browseURL(

+        paste0(

+          "http://www.kegg.jp/kegg-bin/show_pathway?",

+          pathway,

+          '/',

+          n,

+          collapse = ''

+        )

       )

-    )

     }

   }

@@ -567,5 +572,5 @@ getReactomeDiagram <- function(mrnaObject, pathway, imageFormat) {

       n

     )

   if(identical(interactive(), TRUE))

-   browseURL(a)

+    browseURL(a)

 }

@@ -27,7 +27,74 @@ commonGene <- function(mrnaobject,

   tmp <- big_islands[S4Vectors::queryHits(hits), ]

   tmp1 <- aa[S4Vectors::subjectHits(hits), ]

-  pairss <- rbind(pairss, data.frame(tmp$gene, tmp1$gene))

+  pairss <- unique(rbind(pairss, data.frame(tmp$gene, tmp1$gene)))

+  

+  getNoncode <- function(x) {

+    a <-

+      pairss[which(pairss[, 2] %in% unlist(mrnaobject@geneList[[x]])), 1]

+    a[!duplicated(a)]

+  }

+  

+  ab <- lapply(seq_along(mrnaobject@Term), getNoncode)

+  

+  ab[IRanges::isEmpty(ab)] <- 'NA'

+  if (length(mrnaobject@geneList) == 1)

+    ab <- list(ab)

+  return(ab)

+}

+commonGeneRegion <- function(mrnaobject,

+                             org_assembly,

+                             downstream,

+                             upstream,

+                             inRegion) {

+  a <- unique(unlist(mrnaobject@geneList))

+  aa <-

+    convertGeneID(genelist = a,

+                  genetype = 'NCBI',

+                  org_assembly = org_assembly)

+  

+  regions <- paste(sub('chr','',seqlevels(inRegion)), start(inRegion), end(inRegion), sep=":")

+  if(org_assembly == 'hg19' | org_assembly == 'hg38'){

+    results <- getBM(attributes = c( "chromosome_name", "start_position","end_position", 'strand', "hgnc_symbol"),

+                     filters = c("chromosomal_region"),

+                     values=regions,

+                     mart=pkg.env$mart)

+  }else{

+    results <- getBM(attributes = c( "chromosome_name", "start_position","end_position", 'strand', "external_gene_name"),

+                     filters = c("chromosomal_region"),

+                     values=regions,

+                     mart=pkg.env$mart)

+  }

+  

+  colnames(results)[5] = 'hgnc_symbol'

+  

+  for(i in 1 : dim(results)){

+    if(results$hgnc_symbol[i] == ''){

+      results$hgnc_symbol[i] = paste0('chr',results$chromosome_name, ':', results$start_position,'-', results$end_position)

+    }}

+  

+  file1 <-

+    with(results, GRanges(

+      paste0("chr", chromosome_name),

+      IRanges::IRanges(start_position, end_position),

+      strand,

+      hgnc_symbol

+    ))

+  

+  big_islands <-

+    resize(file1, width = upstream + width(inRegion), fix = "start")

+  hits <- findOverlaps(big_islands, aa, ignore.strand = TRUE)

+  tmp <- big_islands[S4Vectors::queryHits(hits), ]

+  tmp1 <- aa[S4Vectors::subjectHits(hits), ]

+  pairss <- data.frame(tmp$hgnc_symbol, tmp1$gene)

+  

+  big_islands <-

+    resize(file1, width = downstream + width(inRegion), fix = "end")

+  hits <- findOverlaps(big_islands, aa, ignore.strand = TRUE)

+  tmp <- big_islands[S4Vectors::queryHits(hits), ]

+  tmp1 <- aa[S4Vectors::subjectHits(hits), ]

+  

+  pairss <- unique(rbind(pairss, data.frame(tmp$hgnc_symbol, tmp1$gene)))

   getNoncode <- function(x) {

     a <-

@@ -9,8 +9,7 @@ getmiRNACount(mirnagene, cancer, databaseFile)

 \arguments{

 \item{mirnagene}{Data frame of the mature format}

-\item{cancer}{Name of the TCGA project code such as 'BRCA' that is

-analyzed for miRNA-mRNA correlation}

+\item{cancer}{Name of the TCGA project code such as 'BRCA'}

 \item{databaseFile}{Path of miRcancer.db file}

 }

@@ -23,3 +23,10 @@ Give top n enrichment results

 Number of top enrichment results of the pathway or GO terms for the given

 object and the order type - p-value or adjusted p-value.

 }

+\examples{

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

+   near=TRUE, genetype = 'Ensembl_gene')

+   

+result = topEnrichment(mrnaObject = ncGO, type = "pvalue", n = 10)

+

+}