View source: R/compare_enrich.R
compare_enrich | R Documentation |
Function to run over representation analysis on your hits and return a plot that compare the pathways found between your treatments.
compare_enrich(
hits,
gene_column = "Gene",
treatment_column = NULL,
species = c("human", "mouse"),
n_pathway = 5,
pval_cutoff = 0.01,
minGSSize = 3,
database = c("WikiPathway", "KEGG", "GO", "CETSA")
)
hits |
The hitlist; a data.frame containing the genes id and preferably a treatment column but not necessary. |
gene_column |
The name of the coulumn that contains the genes. Default is 'Gene'. |
treatment_column |
The name of the column that contains the treatments. Default is NULL. |
species |
Specify the species. Currently, only 'human' and 'mouse' are available. |
n_pathway |
Number of pathway to show on plot. Default is 5.
For more info you, see |
pval_cutoff |
The p-value cutoff for the enrichment analysis. |
minGSSize |
minimal size of each gene set for analyzing. Default here is 3 |
database |
Specify the database. Currently, WikiPathway, KEGG, GO and CETSA are available. |
A list that contains the results and the plot.
clusterProfiler
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