genePathwayEnricher: Given genes that fall in the given upstream and downstream...

In guldenolgun/NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Given genes that fall in the given upstream and downstream region of mRNAs of interest, pathway enrichment analysis is carried out

Description

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", "Ensembl_gene", "Ensembl_trans", "NCBI"),
  near = TRUE,
  isTADSearch = FALSE,
  TAD = tad_hg19,
  gmtName = "",
  express = FALSE,
  isCustomExp = FALSE,
  cancer,
  exp1,
  exp2,
  label1 = "",
  label2 = "",
  isUnionCorGene = FALSE,
  databaseFile,
  isGeneEnrich = FALSE
)

Arguments

gene	Input noncoding genes other than miRNA
org_assembly	Genome assembly of interest for the analysis. Possible assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and "hg38" for human
genetype	Type of the input gene list. Possible values are "Entrez", "mirna", "Ensembl_gene", "Ensembl_trans", "NCBI". For HUGO gene symbol "NCBI" value, for Entrez gene id "Entrez", for mirbase id "mirna" is used.
near	Boolean value presents whether cis-neighbourhood should be considered in the analysis
isTADSearch	Boolean value that shows whether TAD analysis is performed. This value has to be TRUE for TAD analysis.
TAD	TAD genomic regions for the species. Predefined TAD regions or any new TAD regions can be used for the analysis. TAD regions must be formated as GRanges object. Predefined TAD regions are 'tad_hg19', 'tad_hg38', 'tad_mm10', 'tad_dmel' for hg19, hg38, mm9 and dm6 assembly, respectively.
gmtName	Custom pathway gmt file
express	Boolean variable whether co-expression analysis is performed. If this option is set to TRUE, co-expression analysis will be performed.
isCustomExp	Boolean variable whether co-expression analysis with custom data will be performed. When this option is set, exp1 and exp2 parameters must be defined.
cancer	Defines the name of the TCGA project code such as 'BRCA' for correlation analysis. Possible cancer types ACC, BLCA, BRCA, CESC, CHOL,COAD, COADREAD, DLBC, ESCA, GBMLGG, HNSC, KICH, KIPAN, KIRC, KIRP, LIHC, LUAD, LUSC, OV, PAAD, PCPG, PRAD, READ, SARC, SKCM, STAD, STES, TGCT, THCA, THYM, UCEC, UCS, UVM, LGG
exp1	Custom expression data matrix. Columns must be genes and rows must be patients. If gene names are provided as header, no need to redefine the headers(labels) of the expression data.
exp2	Custom expression data matrix. Columns must be genes and rows must be patients. If gene names are provided as header, no need to redefine the headers(labels) of the expression data.
label1	Gene names of the custom exp1 expression data. If it is not provided, column name of the exp1 data will be taken.
label2	Gene names of the custom exp2 expression data. If it is not provided, column name of the exp2 data will be taken.
isUnionCorGene	Boolean value that shows whether union of the output of the co-expression analysis and the other analysis should be considered
databaseFile	Path of miRcancer.db file
isGeneEnrich	Boolean value whether gene enrichment should be performed

Value

Pathway enrichment object for the given input

Examples

## Not run: 
#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')
## End(Not run)

guldenolgun/NoRCE documentation built on Oct. 21, 2022, 11:48 a.m.