geneRegionPathwayEnricher: Given gene regions that fall in the given upstream and...

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

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

Description

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,
  isTADSearch = FALSE,
  TAD = tad_hg19,
  gmtName = "",
  express = FALSE,
  isCustomExp = FALSE,
  cancer,
  exp1,
  exp2,
  label1 = "",
  label2 = "",
  isUnionCorGene = FALSE,
  databaseFile,
  isGeneEnrich = FALSE
)

Arguments

region	Bed format of input gene regions other than miRNA. Input must be Granges object.
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
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, LGG, LIHC, LUAD, LUSC, OV, PAAD, PCPG, PRAD, READ, SARC, SKCM, STAD, STES, TGCT, THCA, THYM, UCEC, UCS, UVM
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 of the given input

Examples

## Not run: 
regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")
regionNC <- rtracklayer::import(regions, format = "BED")
ncPath<-geneRegionPathwayEnricher(region = regionNC,
                                  org_assembly = 'hg19',
                                  near = TRUE) 
## End(Not run)

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