WikiEnrichment {NoRCE} | R Documentation

## WikiPathways Enrichment

### Description

WikiPathways Enrichment

### Usage

    WikiEnrichment(
      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

Wiki Pathway Enrichment

### Examples

    a <- WikiEnrichment(genes = breastmRNA,org_assembly = "hg19")

[Package NoRCE version 0.99.26 Index]