candidate_methylated_genes: Select candidate methylation genes

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

Select candidate methylation genes

Description

Select candidate methylation genes from multiple concerned groups.

Usage

candidate_methylated_genes(group_methylation,
                           method,
                           threshod)

Arguments

group_methylation	A list includes the methylation level of each genes obtained by gene_methy_level_distdecay function from multiple concerned groups.
method	A character specifies the method of selecting candidate genes, which incudes median absolute deviation ("MAD") method, differential methylation method ("DM") and obtaines longitudinal methylation genes ("longitudinal methylation").
threshod	A numeric specifies the threshod for different methods to select candidate genes. In method="MAD", the threshod is set "threshod=0.3" by default. In method="DM" context, the threshod is the p-value threshod setting as "threshod=0.05" by default. In "longitudinal methylation" method, the threshod is the p-value threshod setting as "threshod=0.05" by default to select time correlated methylation genes.

Value

It will report a data.frame including the methylation level of each candidate genes in multiple groups.

Examples

## Not run: 
###select candidate methylated genes with high variable methylation genes (e.g. MAD>0.3)
Group_methylation <- list(Group1_methy=Group1_methylevel_distdecay,
                          Group2_methy=Group2_methylevel_distdecay,
                          Group3_methy=Group3_methylevel_distdecay)
select_methylated_genes <- candidate_methylated_genes(group_methylation=Group_methylation,
                                                      method="MAD",threshod=0.3)

## End(Not run)

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