README.md

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

LeukocyteDMGs

LeukocyteDMGs is an algorithm to identify of leukocyte differential genes in methylation array data.

Install

To install the LeukocyteDMGs, install from github using devtools:

library(devtools)
install_github("FunMoy/LeukocyteDMGs")

How to generate simulated data

The simulated data was used to evaluate the performance of LeukocyteDMGs. The program of simudata was used to generate simulated data, and the detailed description was shown in the manual page of simudata. We used an example to explain the simulation experiment:

library(LeukocyteDMGs)
data(mye_and_lym_methy_450k)
data(mye_and_lym_methy_850k)
###Normal and disease blood methylation profiles were simulated, with the proportion of myeloid and lymphocyte in disease blood being 0.6 and 0.4.
simu <- simudata(data = control,refergene = refergene)

Identify individualized and population-level DMGs

The program of LeukocyteDMGs was the main program in our algorithm. LeukocyteDMGs could identify individualized DMGs of disease samples. After identifying individualized DMGs in disease samples, LeukocyteDMGs can infer population-level DMGs, using binomial test. This may meet the different analysis needs of users.

Usage

LeukocyteDMGs(platform,disease,normal,degene,freq,single_fdr,DMGs_fdr) Arguments|Description :--|:--- platform|Methylation data platform used(450 or 850). disease|The dataframe of disease 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 dataframe of normal 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_fdr|The threshold of FDR for identifying individual-level differentially methylation genes. DMGs_fdr|The threshold of FDR for identifying leukocyte differential methylation genes.}

Example

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

Contact email

Please don't hesitate to address comments/questions/suggestions regarding this R package to: Qi Fan [e-mail]; Haidan Yan [e-mail]

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