Get_DM_peakinfor: Detect differential RNA methylation sites.

In NWPU-903PR/m6Aexpress: Predicting context-specific m6A regulation of gene expression

Description

This function is to detect differential RNA methylation sites between two conditions by qnbtest from QNB R package.

Usage

DM_detect(peak_inform,
          DM_CUTOFF_TYPE=pavlue,
          num_ctl,
          diff_peak_pvalue,
          diff_peak_fdr
          )

Arguments

peak_inform	A list data format, one is a dataframe within the consistent peak sites information (e.g. "gene name","seqname","start","end","strand", reads count in each peak of each input samples), another is a vector with libray sizes factor to normalize methylation level of each peak site in further analysis.
DM_CUTOFF_TYPE	A string, such as "pvalue", which specifies the tpye of cut-off to identify differential expression gene, default: DE_CUTOFF_TYPE="pvalue".
num_ctl	A string,such as "2", which specifices the number of samples in control condition.
diff_peak_pvalue	a decimal number, which specifies the p-value cut-off to identify differential methylation peak sites, default: diff_peak_pvalue=0.05.
diff_peak_fdr	a decimal number, which specifies the fdr cut-off to identify differential methylation peak sites, e.g. diff_peak_fdr=0.05.

Value

Results will return a list including the information differential methylation site in dataframe format and a library size factor in vector format.

DM_peak_infor	A dataframe including the information of differential methylation sites
size_factor	A float vector, which specifices the library size factor for IP samples

References

Liu, Lian, et al. "QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model." BMC bioinformatics 18.1 (2017): 1-12.

See Also

qnbtest

Examples

## Not run: 
##Get consist peak site
Get_peak_infor <- Get_peak_sites(IP_BAM, INPUT_BAM,GENE_ANNO_GTF=gtf)
##Detect differential peak sites
DM_sites_infor <- DM_detect(peak_inform=Get_peak_infor,DM_CUTOFF_TYPE=pvalue,num_ctl=2,
                            diff_peak_pvalue=0.05)

## End(Not run)

NWPU-903PR/m6Aexpress documentation built on Dec. 17, 2021, 5:18 a.m.