KeggEnrichment: KEGG pathway enrichment

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

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.