obtain_initial_parameters: Obtain initial parameters

In NWPU-903PR/m6AexpressBHM: m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

Obtain initial parameters

Description

Obtain initial model parameters.

Usage

obtain_initial_parameters(gene_expre_methy,
                          num_group,
                          size_factor)

Arguments

gene_expre_methy	a data.frame including the matched gene expression and methylation level for each sample in all concerned groups.
num_group	a integer giving the number of concerned groups.
size_factor	a numeric vector specifying the sequencing depth size factors for each Input samples.

Value

It will return a list including three components:

b_infor	a data.frame including the random effects value and their corresponding variance, which reflects the variation of gene expression across different concerned groups
coeff_infor	a data.frame inclduing the columns of the initially predicting Beta0, Beta1, alpha. Beta0 is a gene-specific intercept that models the baseline log gene expression. Beta1 captures the influece of m6A methylation on gene expression in all concerned groups. alpha is a gene-specific dispersion parameter in negative binomial regression model.
gene_name	a character vector inclduing the gene symbol or gene name

Examples

## Not run: 
##the match gene reads count and methylation level
gene_reads_methy <- gene_expr_methy$gene_expr_methy
##library size factor for each gene expression data
size_factor <- gene_expr_methy$library_sizefactor
##Obtain the initail model parameters
initial_model_param <- obtain_initial_parameters(gene_expre_methy=gene_reads_methy,
                                                 num_group=3,size_factor=size_factor)

## End(Not run)

NWPU-903PR/m6AexpressBHM documentation built on May 29, 2022, 11:07 p.m.