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

 Package: NoRCE

 Type: Package

 Title: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

-Version: 0.99.19

+Version: 0.99.20

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

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

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

@@ -59,6 +59,8 @@ importFrom(GenomicRanges,split)

 importFrom(GenomicRanges,start)

 importFrom(GenomicRanges,strand)

 importFrom(GenomicRanges,width)

+importFrom(IRanges,IRanges)

+importFrom(IRanges,subsetByOverlaps)

 importFrom(biomaRt,getBM)

 importFrom(biomaRt,useEnsembl)

 importFrom(biomaRt,useMart)

@@ -43,7 +43,7 @@ extractBiotype <- function(gtfFile) {

   a <- data.frame()

   for (i in seq_along(r)) {

     tr <- which(r[[i]] == 'TRUE')

-    a[i, 1:2] <- temp[[i]][tr]

+    a[i, seq_len(2)] <- temp[[i]][tr]

   }

   #gtf <- gsub("^.* ", "", mat, perl = TRUE)

@@ -53,8 +53,8 @@ corrbased <- function(mirnagene,

   return(dat)

 }

-#' Pearson correlation coefficient value of the mRNA genes between miRNA:mRNA

-#' for a given correlation cut-off and cancer.

+#' Pearson correlation coefficient value of the mRNA genes between 

+#' miRNA:mRNA for a given correlation cut-off and cancer.

 #'

 #' @param mRNAgene Data frame of the mRNA genes

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

@@ -1,5 +1,5 @@

-#' Given genes that fall in a given upstream and downstream region of mRNAs of

-#' interest, GO term enrichment analysis is carried out

+#' Given genes that fall in a given upstream and downstream region of 

+#' mRNAs of interest, GO term enrichment analysis is carried out

 #'

 #' @param gene Input genes other than miRNA

 #' @param org_assembly Genome assembly of interest for the analysis. Possible

@@ -44,8 +44,9 @@

 #' @param label2 Gene names of the custom exp2 expression data. If it is not

 #'      provided, column name of the exp2 data will be taken.

 #' @param databaseFile Path of miRcancer.db file

-#' @param isUnionCorGene Boolean value that shows whether union of the output of

-#'       the co-expression analysis and the other analysis should be considered

+#' @param isUnionCorGene Boolean value that shows whether union of the output

+#'      of the co-expression analysis and the other analysis should be 

+#'      considered

 #'

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

 #'

@@ -247,8 +248,8 @@ geneGOEnricher <-

     }

   }

-#' Given genes that fall in the given upstream and downstream region of mRNAs

-#' of interest, pathway enrichment analysis is carried out

+#' Given genes that fall in the given upstream and downstream region of 

+#' mRNAs of interest, pathway enrichment analysis is carried out

 #'

 #' @param gene Input noncoding genes other than miRNA

 #' @param org_assembly Genome assembly of interest for the analysis. Possible

@@ -528,8 +529,8 @@ genePathwayEnricher <-

     }

   }

-#' Given gene regions that fall in the given upstream and downstream region of

-#' mRNAs of interest, GO term enrichment analysis is carried out

+#' Given gene regions that fall in the given upstream and downstream region

+#' of mRNAs of interest, GO term enrichment analysis is carried out

 #'

 #' @param region Bed format of the input gene regions other than miRNA

 #' @param org_assembly Genome assembly of interest for the analysis. Possible

@@ -743,8 +744,8 @@ geneRegionGOEnricher <-

     }

   }

-#' Given gene regions that fall in the given upstream and downstream region of

-#' mRNAs of interest, pathway enrichment analysis is carried out

+#' Given gene regions that fall in the given upstream and downstream region

+#' of mRNAs of interest, pathway enrichment analysis is carried out

 #'

 #' @param region Bed format of input gene regions other than miRNA. Input must

 #'      be Granges object.

@@ -44,6 +44,7 @@ pkg.env$isSymbol = FALSE

 #' @importFrom biomaRt getBM useEnsembl useMart

 #' @importFrom rtracklayer browserSession genome getTable ucscTableQuery

 #' @importFrom rtracklayer genome<-

+#' @importFrom IRanges IRanges

 #'

 #' @examples

 #'

@@ -193,7 +194,7 @@ assembly <- function(org_assembly = c("hg19",

   }

   colnames(data) <- c('chr', 'strand', 'start', 'end', 'symbol')

   ucsc <-

-    with(data, GRanges(chr, IRanges(start, end), strand, symbol))

+    with(data, GRanges(chr, IRanges::IRanges(start, end), strand, symbol))

   pkg.env$ucsc <- ucsc

   td <-

     paste0("TxDb.", types[index, 1], ".UCSC.", types[index, 2], ".",

@@ -548,6 +549,7 @@ getTADOverlap <-

 #' @return GRange object of the given input

 #'

 #' @importFrom biomaRt getBM

+#' @importFrom IRanges IRanges

 #'

 #' @examples

 #'

@@ -669,7 +671,7 @@ convertGeneID <-

     file1 <-

       with(output, GRanges(

         paste0("chr", chromosome_name),

-        IRanges(start_position, end_position),

+        IRanges::IRanges(start_position, end_position),

         '*',

         gene

       ))

@@ -1255,12 +1255,14 @@ predictmiTargets <- function(gene, type, org_assembly)

   else{

     colnames(where) <- c('genesEns', 'genesHugo', 'geneTrans', 'mirna')

     tmp1 <-

-      data.frame(trans = unlist(apply((where[, 3]), 2, strsplit, '[.]'))[2 *

-                                                                           (seq_len(nrow(where))) - 1])

+      data.frame(

+        trans = unlist(apply((where[, 3]), 2, 

+                             strsplit, '[.]'))[2 *(seq_len(nrow(where))) - 1])

     tmp2 <-

-      data.frame(gene =

-                   unlist(apply((where[, 1]), 2, strsplit, '[.]'))[2 *

-                                                                     (seq_len(nrow(where))) - 1])

+      data.frame(

+        gene =unlist(

+          apply((

+            where[, 1]), 2, strsplit, '[.]'))[2 *(seq_len(nrow(where))) - 1])

     dat <-

       cbind.data.frame(tmp1, where$genesHugo, tmp2, where$mirna)

     return(dat)

@@ -109,7 +109,8 @@ KeggEnrichment <-

       {

         enric <-

           c(enric,

-            setNames(list(as.character(r[which(pathT[i] == r$pathway),]$symbol)),

+            setNames(list(

+              as.character(r[which(pathT[i] == r$pathway),]$symbol)),

                      paste(pathT[i])))

       }

     }

@@ -246,7 +247,8 @@ reactomeEnrichment <-

       {

         enric <-

           c(enric,

-            setNames(list(as.character(r[which(pathT[i] == r$pathway),]$symbol)),

+            setNames(

+              list(as.character(r[which(pathT[i] == r$pathway),]$symbol)),

                      paste(pathT[i])))

       }

     }

@@ -454,16 +456,16 @@ WikiPathwayDB <- function(org_assembly = c("hg19",

                                             format = "gmt")

   if (org_assembly == 'dm6')

     wp.gmt <-

-      rWikiPathways::downloadPathwayArchive(organism = "Drosophila melanogaster",

-                                            format = "gmt")

+      rWikiPathways::downloadPathwayArchive(

+        organism = "Drosophila melanogaster",format = "gmt")

   if (org_assembly == 'ce11')

     wp.gmt <-

-      rWikiPathways::downloadPathwayArchive(organism = "Caenorhabditis elegans",

-                                            format = "gmt")

+      rWikiPathways::downloadPathwayArchive(

+        organism = "Caenorhabditis elegans",format = "gmt")

   if (org_assembly == 'sc3')

     wp.gmt <-

-      rWikiPathways::downloadPathwayArchive(organism = "Saccharomyces cerevisiae",

-                                            format = "gmt")

+      rWikiPathways::downloadPathwayArchive(

+        organism = "Saccharomyces cerevisiae",format = "gmt")

   gmtFile <- convertGMT(gmtName = wp.gmt)

   tmp <-

@@ -584,7 +586,8 @@ WikiEnrichment <- function(genes,

     if (length(which(pathT[i] == r$pathID)) > 0)

     {

       enric <-

-        c(enric, setNames(list(as.character(r[which(pathT[i] == r$pathID),]$gene)),

+        c(enric, setNames(

+          list(as.character(r[which(pathT[i] == r$pathID),]$gene)),

                           paste(pathT[i])))

     }

   }

@@ -732,7 +735,8 @@ pathwayEnrichment <- function(genes,

   {

     if (length(which(pathT[i] == r$pathTerm)) > 0)

       enric <-

-        c(enric, setNames(list(as.character(r[which(pathT[i] == r$pathTerm),]$symbol)),

+        c(enric, setNames(

+          list(as.character(r[which(pathT[i] == r$pathTerm),]$symbol)),

                           paste(pathT[i])))

   }

   return(

@@ -234,7 +234,8 @@ topEnrichment <- function(mrnaObject, type, n) {

 #'

 #' @return Network

 #' 

-#' @importFrom igraph cluster_optimal degree graph_from_data_frame layout_with_fr norm_coords V E V<- E<-

+#' @importFrom igraph cluster_optimal degree graph_from_data_frame 

+#' @importFrom igraph layout_with_fr norm_coords V E V<- E<-

 #' @importFrom ggplot2 aes element_text geom_point ggplot labs theme theme_bw

 #'

 #' @export

@@ -353,8 +354,8 @@ createNetwork <-

     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

+#' 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

 #'

 #' @param mrnaObject Output of enrichment results

 #' @param type Sort in terms of p-values or FDR. possible values "pvalue",

@@ -521,8 +522,8 @@ getKeggDiagram <-

   }

 #' Display the enriched Reactome diagram of the given Reactome pathway id.

-#' This function is specific to only one pathway id and identifies the enriched

-#'  genes in the diagram.

+#' This function is specific to only one pathway id and identifies the 

+#' enriched genes in the diagram.

 #'

 #' @param mrnaObject Output of enrichment results

 #' @param pathway Reactome pathway term

@@ -2,8 +2,8 @@

 % Please edit documentation in R/expressionBased.R

 \name{corrbasedMrna}

 \alias{corrbasedMrna}

-\title{Pearson correlation coefficient value of the mRNA genes between miRNA:mRNA

-for a given correlation cut-off and cancer.}

+\title{Pearson correlation coefficient value of the mRNA genes between 

+miRNA:mRNA for a given correlation cut-off and cancer.}

 \usage{

 corrbasedMrna(mRNAgene, cancer, minAbsCor, databaseFile)

 }

@@ -25,6 +25,6 @@ the miRNA-mRNA}

 Data frame of the miRNA-mRNA correlation result

 }

 \description{

-Pearson correlation coefficient value of the mRNA genes between miRNA:mRNA

-for a given correlation cut-off and cancer.

+Pearson correlation coefficient value of the mRNA genes between 

+miRNA:mRNA for a given correlation cut-off and cancer.

 }

@@ -2,8 +2,8 @@

 % Please edit documentation in R/geneEnrichment.R

 \name{geneGOEnricher}

 \alias{geneGOEnricher}

-\title{Given genes that fall in a given upstream and downstream region of mRNAs of

-interest, GO term enrichment analysis is carried out}

+\title{Given genes that fall in a given upstream and downstream region of 

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

 \usage{

 geneGOEnricher(gene, org_assembly = c("hg19", "hg38", "mm10", "dre10",

   "rn6", "dm6", "ce11", "sc3"), genetype = c("Entrez", "mirna",

@@ -71,8 +71,9 @@ provided, column name of the exp1 data will be taken.}

 \item{label2}{Gene names of the custom exp2 expression data. If it is not

 provided, column name of the exp2 data will be taken.}

-\item{isUnionCorGene}{Boolean value that shows whether union of the output of

-the co-expression analysis and the other analysis should be considered}

+\item{isUnionCorGene}{Boolean value that shows whether union of the output

+of the co-expression analysis and the other analysis should be 

+considered}

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

 }

@@ -80,8 +81,8 @@ the co-expression analysis and the other analysis should be considered}

 GO term enrichment object for the given input

 }

 \description{

-Given genes that fall in a given upstream and downstream region of mRNAs of

-interest, GO term enrichment analysis is carried out

+Given genes that fall in a given upstream and downstream region of 

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

 }

 \examples{

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

@@ -2,8 +2,8 @@

 % Please edit documentation in R/geneEnrichment.R

 \name{genePathwayEnricher}

 \alias{genePathwayEnricher}

-\title{Given genes that fall in the given upstream and downstream region of mRNAs

-of interest, pathway enrichment analysis is carried out}

+\title{Given genes that fall in the given upstream and downstream region of 

+mRNAs of interest, pathway enrichment analysis is carried out}

 \usage{

 genePathwayEnricher(gene, org_assembly = c("hg19", "hg38", "mm10",

   "dre10", "rn6", "dm6", "ce11", "sc3"), genetype = c("Entrez", "mirna",

@@ -81,8 +81,8 @@ performed}

 Pathway enrichment object for the given input

 }

 \description{

-Given genes that fall in the given upstream and downstream region of mRNAs

-of interest, pathway enrichment analysis is carried out

+Given genes that fall in the given upstream and downstream region of 

+mRNAs of interest, pathway enrichment analysis is carried out

 }

 \examples{

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

@@ -2,8 +2,8 @@

 % Please edit documentation in R/geneEnrichment.R

 \name{geneRegionGOEnricher}

 \alias{geneRegionGOEnricher}

-\title{Given gene regions that fall in the given upstream and downstream region of

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

+\title{Given gene regions that fall in the given upstream and downstream region

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

 \usage{

 geneRegionGOEnricher(region, org_assembly = c("hg19", "hg38", "mm10",

   "dre10", "rn6", "dm6", "ce11", "sc3"), near = TRUE, backG = "",

@@ -76,8 +76,8 @@ considered}

 GO term enrichment object for the given input

 }

 \description{

-Given gene regions that fall in the given upstream and downstream region of

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

+Given gene regions that fall in the given upstream and downstream region

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

 }

 \examples{

@@ -2,8 +2,8 @@

 % Please edit documentation in R/geneEnrichment.R

 \name{geneRegionPathwayEnricher}

 \alias{geneRegionPathwayEnricher}

-\title{Given gene regions that fall in the given upstream and downstream region of

-mRNAs of interest, pathway enrichment analysis is carried out}

+\title{Given gene regions that fall in the given upstream and downstream region

+of mRNAs of interest, pathway enrichment analysis is carried out}

 \usage{

 geneRegionPathwayEnricher(region, org_assembly = c("hg19", "hg38",

   "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"), near = FALSE,

@@ -76,8 +76,8 @@ performed}

 Pathway enrichment object of the given input

 }

 \description{

-Given gene regions that fall in the given upstream and downstream region of

-mRNAs of interest, pathway enrichment analysis is carried out

+Given gene regions that fall in the given upstream and downstream region

+of mRNAs of interest, pathway enrichment analysis is carried out

 }

 \examples{

@@ -2,8 +2,8 @@

 % Please edit documentation in R/plot.R

 \name{getGoDag}

 \alias{getGoDag}

-\title{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}

+\title{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}

 \usage{

 getGoDag(mrnaObject, type, n, filename, imageFormat, p_range = seq(0,

   0.05, by = 0.001))

@@ -27,8 +27,8 @@ getGoDag(mrnaObject, type, n, filename, imageFormat, p_range = seq(0,

 Saves image file in a given format

 }

 \description{

-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

+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

 }

 \examples{

 ncRNAPathway<-mirnaPathwayEnricher(gene = brain_mirna,

@@ -3,8 +3,8 @@

 \name{getReactomeDiagram}

 \alias{getReactomeDiagram}

 \title{Display the enriched Reactome diagram of the given Reactome pathway id.

-This function is specific to only one pathway id and identifies the enriched

- genes in the diagram.}

+This function is specific to only one pathway id and identifies the 

+enriched genes in the diagram.}

 \usage{

 getReactomeDiagram(mrnaObject, pathway, imageFormat)

 }

@@ -21,8 +21,8 @@ Shows reactome diagram marked with an enriched genes in a browser

 }

 \description{

 Display the enriched Reactome diagram of the given Reactome pathway id.

-This function is specific to only one pathway id and identifies the enriched

- genes in the diagram.

+This function is specific to only one pathway id and identifies the 

+enriched genes in the diagram.

 }

 \examples{