CompareMCB: Compare multiple methylation correlated blocks lists

In whirlsyu/EnMCB: Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Compare multiple methylation correlated blocks lists

Description

This function is used to find the Methylation correlated blocks that differentially expressed between groups. This function calculates attractors of all the MCBs among the groups and find the attractor MCBs.

Usage

CompareMCB(
  MCBs,
  method = c("attractors")[1],
  p_value = 0.05,
  min_CpGs = 5,
  platform = "Illumina Methylation 450K"
)

Arguments

MCBs	Methylation correlated blocks list.
method	method used for calculation of differential expression, should be one of "attractors","t-test". Defualt is "attractors".
p_value	p value threshold for the test.
min_CpGs	threshold for minimum CpGs must included in the individual MCBs.
platform	This parameter indicates the platform used to produce the methlyation profile.

Details

Currently, only illumina 450k platform is supported, the methylation profile need to convert into matrix format.

Value

Object of class list with elements:

MCBsites	Character set contains all CpG sites in MCBs.
MCBinformation	Matrix contains the information of results.

Author(s)

Xin Yu

References

Xin Yu, De-Xin Kong, EnMCB: an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models, Bioinformatics, 2021, btab415

Examples

data('demo_data',package = "EnMCB")

whirlsyu/EnMCB documentation built on Jan. 25, 2023, 4:33 a.m.