KeggEnrichment: KEGG pathway enrichment

View source: R/pathway.R

KeggEnrichmentR Documentation

KEGG pathway enrichment

Description

KEGG pathway enrichment

Usage

KeggEnrichment(
  genes,
  org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"),
  pCut = 0.05,
  pAdjCut = 0.05,
  pAdjust = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"),
  min = 5,
  gmtFile = "",
  isSymbol = "",
  isGeneEnrich = ""
)

Arguments

genes

Input genes

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

pCut

Threshold value for the pvalue. Default value is 0.05

pAdjCut

Cutoff value for the adjusted p-values using one of given method. Default value is 0.05.

pAdjust

Methods of the adjusted p-values. Possible methods are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none"

min

Minimum number of genes that are required for enrichment. By default, it is set to 5.

gmtFile

File path of the gmt file

isSymbol

Boolean value that controls the gene formats. If it is TRUE, gene format of the gmt file should be symbol. Otherwise, gene format must be ENTREZ ID.

isGeneEnrich

Boolean value whether gene enrichment should be performed

Value

KEGG pathway enrichment results

Examples

## Not run: 
subsetGene <- breastmRNA[1:30,]

br_enr<-KeggEnrichment(genes = subsetGene,
                       org_assembly='hg19')

## End(Not run)


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