geneGOEnricher: Given genes that fall in a given upstream and downstream...

View source: R/geneEnrichment.R

geneGOEnricherR Documentation

Given genes that fall in a given upstream and downstream region of mRNAs of interest, GO term enrichment analysis is carried out

Description

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", "Ensembl_gene", "Ensembl_trans", "NCBI"),
  backG = "",
  backGType = "pc_gene",
  near = FALSE,
  isTADSearch = FALSE,
  TAD = c(tad_hg19, tad_dmel, tad_hg38, tad_mm10),
  express = FALSE,
  isCustomExp = FALSE,
  cancer,
  exp1,
  exp2,
  label1 = "",
  label2 = "",
  isUnionCorGene = FALSE,
  databaseFile
)

Arguments

gene

Input 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" is used.

backG

The set of genes that tested against to the input (background gene)

backGType

Type of the background gene. If miRNA gene set is used for background gene, backGType should be set to the 'mirna'

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.

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

Value

GO term enrichment object for the given input

Examples

## Not run: 
ncGO<-geneGOEnricher(gene = brain_disorder_ncRNA, org_assembly='hg19',
near=TRUE, genetype = 'Ensembl_gene')

## End(Not run)


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