m6A_express_model: m6Aexpress model

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

Description

Predicate m6A regulated expression gene by m6Aexpress model in specific context.

Usage

m6A_Express_model(Input_file,
                  CUTOFF_TYPE="FDR",pvalue, 
                  FDR,out_dir)

Arguments

Input_file	A list data format, one is a dataframe including the paired reads count and methylation intensity for each gene in each samples; another is a vector with libray sizes factor for INPUT samples used to normalized the gene expression for INPUT samples.
CUTOFF_TYPE	A string, such as "FDR", which specifies the tpye of cut-off to identify significant m6A regulated express gene (m6-reg-exp gene), default: CUTOFF_TYPE="FDR".
pvalue	a decimal number, which specifies the p-value cut-off in the predicting m6A regulated expression gene of m6A-express model.
FDR	a decimal number, which specifies the FDR cut-off in the predicting m6A regulated expression gene of m6A-express model, default: 0.05.
out_dir	A string, which specify the output directory, default: out_dir=NA, the output result will save in the current directory. Otherwise, m6A_express will output the significant m6A regulated expression gene under given cutoff, e.g. FDR<0.05 or pvalue<0.05.

Details

This function is used to predicate m6A regulated expression gene by m6Aexpress model, which is based on a Bayesian Hierical Negative Binomial Regression model. Parts of model is accomplished by calling python codel in the extradata folder of these package.

Value

The predicting m6A methylation regulated expression (m6A-reg-exp) genes under given cut-off in .XLS (tab-delimited) format file. The .XLS file includes five columns: the name of m6A-reg-exp gene, Beta0, Beta1, pvalue and FDR.

gene_name	The name of m6A methylation regulated expression gene in the given annotation file.
Beta0	Beta0 is a gene-specific intercept and models the baseline log gene expression.
Beta1	Beta1 captures the influence of m6A methylation on gene expression.
pvalue	pvalue of the predicted m6A-reg-exp genes.
FDR	FDR of the predicted m6A-reg-exp genes.

Author(s)

Teng Zhang <[e-mail]>

Examples

## Not run: 
##match gene expression and methylation intensity of HVP gene
expr_methy_gene <- match_expr_methy(gene_expre_infor=get_gene_express, 
                                     gene_methy_infor=gene_methyintensity,
                                   OUTPUT_DIR=NA)
##predicate m6A-reg-exp gene
m6A_Express_model(Input_file=expr_methy_gene,
                  CUTOFF_TYPE="FDR", 
                  FDR=0.05)

## End(Not run)

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