get.enriched.pw {Pigengene}R Documentation

Performs pathway over representation analysis

Description

Takes as input a vector or list of gene IDs in any convention, and performs over representation analysis.

Usage

get.enriched.pw(genes, idType, pathwayDb, ont=c("BP", "MF", "CC"),
                Org="Human", OrgDb=NULL, outPath, pvalueCutoff=0.05, 
                pAdjustMethod="BH", fontSize=14, verbose=0)

Arguments

genes

A character vector or a named list of genes for which pathway over representation analysis to be done.

idType

A string describing the type of input gene ID e.g., "ENTREZID", "REFSEQ", "SYMBOL".

pathwayDb

A character vector determining which enrichment database to be used e.g., "GO", "KEGG", "REACTOME", or "NCG".

ont

GO ontology terms to be analysed e.g., "BP", "MF" or "CC". Default is all three.

Org

A character string equal to "Human" or "Mouse" determining the reference organism to be used. For "Human" and "Mouse" org.Hg.eg.db and org.Mm.eg.db will be used, respectively. If Org is not NULL, OrgDb must be NULL.

OrgDb

The reference data base to be used. Use e.g. org.Ce.eg.db for 'Celegans' when analysing Celegans data. If OrgDb is not NULL, Org must be NULL.

outPath

A file path where results will be saved.

pvalueCutoff

A numerical value that determines a cutoff of adjusted pValue.

pAdjustMethod

A string passed to the clusterProfiler::enrichGO function to determine the method for adjusting the p-value. Options include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

fontSize

A numerical value that determines the font size of the y-axis and the title in the plot.

verbose

The integer level of verbosity. 0 means silent and higher values produce more details of computation.

Value

A list:

EnrichResults

A list of output of enrichment analysis for different database analyzed.

noEnrichment

A vector of database names in which no enriched pathways were found.

The output is saved for each selected module under the “moduleName\_enrichment” folder. There is a subfolder that includes an excel file and plot(s). Each sheet in the excel file corresponds to a pathway database (KEGG in the below example). Each row is an overrepresented pathway.

Author(s)

Isha Mehta, and Habil Zare

References

Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He, clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology 2012, 16(5):284-287

Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479

See Also

enrichGO, enrichKEGG, enrichNCG, enrichPathway

Examples

library(org.Hs.eg.db)
genes <- c("NM_170730", "NM_001013580", "NM_002142", "NM_003417", "NM_000082",
           "NM_006158", "NM_006047", "NM_022356", "NM_003979", "NM_001030", "NM_022872")
p1 <- get.enriched.pw(genes=genes, idType="REFSEQ", pathwayDb="KEGG", Org="Human", 
                      outPath=getwd(), verbose=1)

[Package Pigengene version 1.19.52 Index]