enrichmentplot: Visualization of BP and KEGG pathway enrichment of functional...

In NWPU-903PR/Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes

Description

Visualization of BP and KEGG pathway enrichment of functional DmM genes with 5'UTR, CDS and 3'UTR DmM sites.

Usage

enrichmentplot(fdmgene,
               sigthr = 0.3,
               bp_fdr_thr = 0.05,
               kegg_fdr_thr = 0.05,
               top_terms = 20,
               input_directory = "",
               version = "10",
               species = 9606,
               savepath = NA)

Arguments

fdmgene	A dataframe of functional DmM genes' information. It is generated using fdmdeepm6A function.
sigthr	The threshold of the FDR used to determine whether a DmMGene is a FDmMGene
bp_fdr_thr	The parameter passed to STRINGdb to determine the threshold of fdr to determine significant enriched BP terms
kegg_fdr_thr	The parameter passed to STRINGdb to determine the threshold of fdr to determine significant enriched KEGG pathways
top_terms	The parameter determines the number of top enriched pathways to show
input_directory	The parameter passed to STRINGdb to determine whether all the database files will be downloaded into this directory and the package can then be used off-line
version	The parameter passed to STRINGdb to determine the version used
species	The parameter passed to STRINGdb to determine the species to do enrichment analysis, in defalt it is human
savepath	The file path where to save the result

Details

The enricnment analysis is done using STRINGdb.

Value

By default, enrichmentplot will output results of

1. Heat map of BP and KEGG pathway enrichment of FDmMGenes;

2. xls formate of the heatmap information.

Author(s)

Songyao Zhang

References

Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes.

NWPU-903PR/Funm6AViewer documentation built on April 25, 2021, 4:26 p.m.