pathwayEnrichment: For a given gmt file of a specific pathway database, pathway...

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

For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.

Description

For a given gmt file of a specific pathway database, pathway enrichment can be performed. Function supports Entrez ID and symbol based gmt file.

Usage

pathwayEnrichment(
  genes,
  gmtFile,
  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"),
  isSymbol,
  min = 5,
  isGeneEnrich = FALSE
)

Arguments

genes	Input genes
gmtFile	File path of the gmt file
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"
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.
min	Minimum number of genes that are required for enrichment. By default, it is set to 5.
isGeneEnrich	Boolean value whether gene enrichment should be performed

Value

Pathway Enrichment

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