LeukocyteDMGs: Identification of leukocyte differential genes in methylation...

In FunMoy/LeukocyteDMGs: Identification of leukocyte differential genes in methylation data from blood samples

Identification of leukocyte differential genes in methylation beta value data from blood samples.

Description

LeukocyteDMGs could identify of leukocyte differential genes in methylation beta value data from blood samples.

Usage

LeukocyteDMGs(platform,disease,normal,degene,freq,single_value,DMGs_value,FDR=TRUE)

Arguments

platform	Methylation data platform used(450 or 850).
disease	The methylation beta value dataframe of disease blood sample.The first columns is the gene symbols and the remaining columns are the gene methylation values of the disease samples.The gene symbols must be consistent with the normal.
normal	The methylation beta value dataframe of normal blood sample.The first columns is the gene symbols and the remaining columns are the gene methylation values of the normal samples.The gene symbols must be consistent with the disease.
degene	The differential methylation genes of normal and disease was identified using the T-test.
frep	The criteria for identifying stable gene pairs. The default setting of freq is 0.95.
single_value	The threshold for identifying individual-level differentially methylation genes.
DMGs_value	The threshold for identifying leukocyte differential methylation genes.
FDR	Whether to perform BH correction.The default setting is TRUE.

Value

A list with the following two items.

individual A list with individual-level result.It contains all gene symbols,individual-level DMGs in each case sample (value is 1 for hypermethylated,value is -1 for hypomethylated) and adjusted pvalue using the Benjamini and Hochberg approach.

population A list with population-level DMGs.

Examples

data(example)
DMGs=LeukocyteDMGs(450,disease,normal,degene,0.95,0.05,0.05,FDR = TRUE)

FunMoy/LeukocyteDMGs documentation built on Feb. 22, 2023, 3:27 p.m.