funm6aviewer: Visualization of single base DmM sites and FDmMGenes.

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

Description

This function is used to visualize single base differential m6A methylation sites and functional DmM genes.

Usage

funm6aviewer(dminfo,
             deinfo,
             bamgrlist = NA,
             intrested_gene = NA,
             top_alph = 0.8,
             fungenethr = 0.3,
             permutime = NA,
             descoretype = "pval",
             txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
             orgdb = org.Hs.eg.db,
             orgsymbol = org.Hs.egSYMBOL,
             datapath = NA,
             rescore_thr = 0.8,
             descore_thr = 0.8,
             enrich_input_directory = "",
             version = "10",
             species = 9606,
             bp_fdr_thr = 0.05,
             kegg_fdr_thr = 0.05,
             savepath = NA,
             no_cores = NA)

Arguments

dminfo	A dataframe of DmM sites information. It can be generated using summarydmdeepm6A from DMDeepm6A package result.
deinfo	A dataframe of gene differential expression information
bamgrlist	A list containing the reads count of IP/Input bam files under different condition and the id of each files. It can be generated using makegrreadsfrombam function. This is necessary if users want to watch the reads coverage for interested genes.
intrested_gene	A vector of interested genes to visualize, can be gene entrez id or gene symbol
top_alph	The top percentage threshold used to aggregate the ranks from each PPI network. In defalt, the threshold is set as 0.8 which means only MSB scores larger than 80 pencentage of DE scores will contribute to the functional rank. A larger top_alph (must no more than 1) makes the functional ranks aggregation test more rigorous.
fungenethr	The threshold of the FDR used to determine whether a DmMGene is a FDmMGene
permutime	The permutation times to calculate an empirical p-value for DmMGenes to be FDmMGenes
descoretype	The value used to calculate the DE score. It can be "pval", "padj", or "log2FoldChange" denotes use the p-value, FDR or log2FoldChange of genes to calculate the DE score.
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.
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.
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.
datapath	The file path where the network information required of FunDMDeepm6A, usually do not need to input, only if you prefer to use your own PPI networks
rescore_thr	The threshold of relative MSB score percentage used to determine FDmMGenes with relatively higher MSB score
descore_thr	The threshold of DE score percentage used to determine FDmMGenes with relatively higher MSB score
enrich_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
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
savepath	The file path where to save the result
no_cores	The number of cores used to run the function in parallel

Details

funm6aviewer is the main function of the package which is used to viraulize the single base DmM sites, identify and visualize functional DmM genes in one button. The permutime will influence the accuracy of identified FDmMGenes, more permutation times will generate more reliable result while takes longer time. In default, it is 10^4 and this is usually sufficient and comsumes less time, users can set it larger if the scale of DmM genes is larger.

Value

By default, funm6aviewer will output results of

1. Functional DmM genes information;

2. DmM sites distribution on RNA;

3. Counts of DmM sites on different RNA regions;

4. DmM sites and reads coverage on interested gene;

5. Function enrichment of FDmMGenes;

6. Context specific function of interested genes;

7. DmMGene's MSB score along with DE score;

8. Network of FDmMGene's MSB neighbors.

Author(s)

Songyao Zhang

References

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

Examples

## example using default hg19 genome

dminfo <- system.file("extdata", "DMinfo_toy.xls", package="Funm6AViewer")
deinfo <- system.file("extdata", "DEinfo_toy.xls", package="Funm6AViewer")

dminfo <- read.table(dminfo, header = TRUE, stringsAsFactors = FALSE)
deinfo <- read.delim(deinfo, header = TRUE, stringsAsFactors = FALSE)

bamreadsgr <- system.file("extdata", "bamgrlist_toy.RData", package="Funm6AViewer")
load(bamreadsgr)

siggene <- c("CCNT1", "MYC", "BCL2")
permutime <- 1000

## the datapath and enrich_input_directory are the filepaths where the required
## PPI and function annotation data saved they can be downloaded
## from https://pan.baidu.com/s/1qOGG57OgxmrTwSbbBEeQ2w&shfl=sharepset
datapath <- "E:/Funm6A_package/data"
enrich_input_directory <- "E:/Funm6A_package/data"

re <- funm6aviewer(dminfo, deinfo, grlist, intrested_gene =  siggene, permutime = permutime,
                   datapath = datapath, enrich_input_directory = enrich_input_directory)

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