get.enriched.pw {Pigengene} | R Documentation |
Takes as input a vector or list of gene IDs in any convention, and performs over representation analysis.
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)
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" |
OrgDb |
The reference data base to be used. Use e.g. |
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:: |
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. |
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.
Isha Mehta, and Habil Zare
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
enrichGO
,
enrichKEGG
,
enrichNCG
, enrichPathway
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)