siggenepathplot: 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

siggenepathplot(fdmgene,
                intrested_gene,
                bp_fdr_thr = 0.05,
                kegg_fdr_thr = 0.05,
                orgsymbol = org.Hs.egSYMBOL,
                input_directory = "",
                version = "10",
                species = 9606,
                savepath = NA)

Arguments

fdmgene	A vector of functional DmM genes, can be gene entrez id or gene symbol
intrested_gene	A vector of interested genes to visualize, can be gene entrez id or gene symbol
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
orgsymbol	The gene name annotation. You need to input it similar to "org.Hs.egSYMBOL" if DefaultGenome is use other genomes instead of human genome.
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, siggenepathplot will output results of

1. Plot of the context specific BP and KEGG pathway of interested genes;

2. xls formate of BP and KEGG pathway enrichment terms.

Author(s)

Songyao Zhang

References

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

Examples

## context specific function annotation for interested genes

dminfo <- system.file("extdata", "DMinfo_toy.xls", package="Funm6AViewer")
dminfo <- read.table(dminfo, header = TRUE, stringsAsFactors = FALSE)
fdmgene <- unique(dminfo$name)

siggene <- c("CCNT1", "MYC", "BCL2")

# The input_directory is the parameter passed to string_db, the GO and KEGG function
# annotation data will be downloaded to the setted filepath.
# You can also donwloaded the annotation data previously
# from https://pan.baidu.com/s/1qOGG57OgxmrTwSbbBEeQ2w&shfl=sharepset
# and set the input_directory as where you save the data.
input_directory <- "E:/Funm6A_package/data"

re <- siggenepathplot(fdmgene = fdmgene, intrested_gene = siggene,
                      input_directory = input_directory)

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