Description Usage Arguments Value Author(s) Examples
PathwayEnrichment
a function that perform a pathway enrichment analysis
Return a barplot that show the enriched pathway and its p value(fisher test) that is smaller than
the ajusted p value. The null hypothesis for each fisher test: the pathway
is not enriched in the given gene set.
1 | PathwayEnrichment(geneSet, reactInfo)
|
geneSet |
A list of gene symbol in the system that you want to perform pathway enrichment analysis. |
reactInfo |
a dataframe map the reactome pathway id to the reference gene symbol |
a dataframe that show the enriched pathway, adjusted pa value using Bonferroni and Benjamini-Hochberg methods,and its p value(fisher test).
Yufei Yang (aut)
1 2 3 4 5 6 7 8 | ## Not run:
# Picking sample gene list to find the pathway enrichment and p value
# Call the symComp helper function to generate list
sampleGeneList <- c("CREBBP","NR1H3","RORA","SREBF1","SMARCD3")
reactInfo <- fetchData("ReactomeSym")
result <- PathwayEnrichment(sampleGeneList,reactInfo)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.