add_DEDM_infor: Add DE ad DM information

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

Description

Add the log2foldchange and the degree of differential methylation intensity for m6A-reg-exp gene

Usage

add_LFC_DDM(expre_methyre, 
            DE_gene, 
            methy_intensity,
            num_cond1,OUTPUT_DIR=NA)

Arguments

expre_methyre	A dataframe format, which specifices a set of significant m6A regulated expression genes predicated by m6Aexpress model.
DE_gene	A list including reads count for DE gene, size facor and significant DE gene information. In this function, the log2foldchange of significant DE gene will be used.
methy_intensity	A dataframe with the methylation intensity for each gene of each sample under case-control context.
num_cond1	A integer, such as "2", which specifices the number of samples in the control condition. It will be used to select the methlation intensity samples in control condition.
OUTPUT_DIR	A string, which specify the output directory, default: OUTPUT_DIR=NA, the output result will save in the current directory. Otherwise, add_LFC_DDM will output the specific directory in .xls format.

Details

This function is only used in the differential expression (DE) and differential methylation (DM) context, which will add the log2foldchange of DE gene and the degree of DM to the m6A-reg-exp gene. The degree of DM is defined as the difference of mean methylation intensity between treated and control group.

Value

A dataframe format, which includes the m6A-reg-exp gene information with addded log2foldchagne and the degree of DM.

Author(s)

Teng Zhang <[e-mail]>

Examples

## Not run: 
m6A_express_addLFC_DDM <- add_LFC_DDM(expre_methyre=m6Areg_expr_gene, 
                                    DE_gene=DE_gene, methy_distdecay=DM_methy,
                                    num_cond1=2, OUTPUT_DIR=NA)

## End(Not run)

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