# NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

## Documentation for package ‘NoRCE’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

annGO | Annotate the set of genes with the GO terms for a given species and assembly
assembly | Get the required information for the given assembly
brain_disorder_ncRNA | Differentially expressed non-coding gene
brain_mirna | Differentially expressed human brain data
breastmRNA | Protein coding genes that are differentially expressed in TCGA breast cancer RNAseq data.
calculateCorr | Calculates the correlation coefficient values between two custom expression data.
convertGeneID | Convert gene ids according to the gene type
convertGMT | Convert gmt formatted pathway file to the Pathway ID, Entrez, symbol formatted data frame
corrbased | Pearson correlation coefficient value of the miRNA genes between miRNA:mRNA for a given correlation cut-off and cancer.
corrbasedMrna | Pearson correlation coefficient value of the mRNA genes between miRNA:mRNA for a given correlation cut-off and cancer.
createNetwork | Create interaction network for top n enriched GO term:coding RNA or GO-term:noncoding RNA interaction. Nodes are GO term and RNA, edges are interactions between them. Each GO-term is annotated and enriched with the mRNAs provided from the input list.
drawDotPlot | Draw dot plot of the enrichment object
extractBiotype | Get the biotype of the non-coding genes. It is suitable for the GENCODE gtf files
filterBiotype | Extract the genes that have user provided biotypes. This method is useful when input gene list is mixed or when research of the interest is only focused on specific group of genes.
geneGOEnricher | Given genes that fall in a given upstream and downstream region of mRNAs of interest, GO term enrichment analysis is carried out
genePathwayEnricher | Given genes that fall in the given upstream and downstream region of mRNAs of interest, pathway enrichment analysis is carried out
geneRegionGOEnricher | Given gene regions that fall in the given upstream and downstream region of mRNAs of interest, GO term enrichment analysis is carried out
geneRegionPathwayEnricher | Given gene regions that fall in the given upstream and downstream region of mRNAs of interest, pathway enrichment analysis is carried out
getGoDag | 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
getKeggDiagram | Display the enriched KEGG diagram of the KEGG pathway. This function is specific to only one KEGG pathway id and identifies the enriched genes in the diagram.
getmiRNACount | Get TCGA miRNAseq expression of miRNA genes for the given cancer
getNearToExon | Get only those neighbouring genes that fall within exon region
getNearToIntron | Get only those neighbouring genes that fall within intron region
getReactomeDiagram | 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.
getTADOverlap | For given region of interest, overlapped genes in the TAD regions are found. Results can be filtered according to the available cell lines.
getUCSC | Get nearest genes for the window of the upstream/downstream region.
goEnrichment | Perform enrichment analysis of the given genes
KeggEnrichment | KEGG pathway enrichment
listTAD | List cell line of the given topological domain regions
mirna | Brain miRNA expression retrieved from the TCGA
mirnaGOEnricher | GO term enrichments of the microRNA genes with mRNAs that fall in the given upstream/downstream regions of the microRNA genes
mirnaPathwayEnricher | Pathway enrichments of the microRNA genes with mRNAs that fall in the given upstream/downstream regions of the microRNA genes
mirnaRegionGOEnricher | GO enrichments of the microRNA regions with mRNAs that fall in the given upstream/downstream regions of the microRNA genes
mirnaRegionPathwayEnricher | Pathway enrichments of the microRNA regions with mRNAs that fall in the given upstream/downstream regions of the microRNA genes
mrna | Brain mRNA expression retrieved from the TCGA
ncRegion | Differentially expressed non-coding gene regions
NoRCE-class | An S4 class to represent enrichment
packageCheck | Check the package availability for the given assembly
pathwayEnrichment | For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.
predictmiTargets | Predict the miRNA targets for the miRNA or mRNA genes, which is specified with type parameter
reactomeEnrichment | Reactome pathway enrichment
setParameters | Set the parameters
tad_dmel | TAD regions for the fly
tad_hg19 | TAD regions for human hg19 assembly
tad_hg38 | TAD regions for human hg38 assembly
tad_mm10 | TAD regions for mouse
topEnrichment | 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.
WikiEnrichment | WikiPathways Enrichment
writeEnrichment | Write the tabular form of the pathway or GO term enrichment results