dmsiteplot: Visualization of DmM sites on gene's isoforms.

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

Description

Visualization of DmM sites on gene's isoforms.

Usage

dmsiteplot(dminfo,
           intrested_gene,
           savepath = NA,
           txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
           orgsymbol = org.Hs.egSYMBOL,
           orgdb = org.Hs.eg.db)

Arguments

dminfo	A dataframe of DmM sites information. It can be generated using summarydmdeepm6A from DMDeepm6A package result.
intrested_gene	A vector of interested gene to visualize, can be entrez gene id or gene symbol
savepath	The file path where to save the result
txdb	The txdb famate genome annotation. You need to input it similar to "TxDb.Hsapiens.UCSC.hg19.knownGene" if use other genomes instead of hg19.
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.
orgdb	The annotation of genome. You need to input it similar to "org.Hs.eg.db" if DefaultGenome is use other genomes instead of human genome.

Details

This function is used to visualize DmM sites on interested gene's isoforms.

Value

By default, dmsiteplot will output results of DmM sites on interested gene's isoforms.

Author(s)

Songyao Zhang

References

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

Examples

## dm sites plot for interested genes

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

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

re <- dmsiteplot(dminfo = dminfo, intrested_gene = siggene)

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