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

Description Usage Arguments Value

View source: R/pathway.R

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

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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


NoRCE documentation built on Nov. 8, 2020, 7:17 p.m.