Release Note

Release Note

version	0.0.2
Date	2022-12-06
Maintainer	Yifan Yang [email protected]
Author	Xiaoqin Pan, Yifan Yang

Pairwise methylation association test (PMAT) is a computational tool tailored for identifying DMRs between unordered pairs like twins. In this tool, the absolute methylation difference between unorderd pairs was maximized in DMRs identification. A folded normal (FN) test based on the framework of the likelihood ratio test was proposed recently and implemented to test the methylation difference between unordered pairs in each methylation region. To improve the approximation precision of an FN test when the sample size is not large enough, we further established PMAT with Bartlett correction (PMAT-C). In PMAT-C, a folded normal test with Bartlett correction (FN-C) was implemented to test the methylation differences between unordered pairs.

• PMAT detects the differentially methylated regions.
• PMAT has the same ability as metilene.
• PMAT has the same option as metilene.
• PMAT provides an automatic optimization and an initial value-choosing strategy to perform MLE calculation.

Change log for v 0.0.2

1. PMAT-C

• Bartlett Correction for Folded Normal;
• Output FDR (B-H) for FN p-value;
• Other p-value corrections;

2. Documentation and Demos for PMAT.

0.0.1

Release Note

version	0.0.1
Date	2022-11-22
Maintainer	Yifan Yang [email protected]
Author	Xiaoqin Pan, Yifan Yang

PMAT detects the differentially methylated regions. It solves the twin-pair problem using tools such as metilene.

• PMAT detects the differentially methylated regions.
• PMAT has the same ability as metilene.
• PMAT has the same option as metilene.
• PMAT provides an automatic optimization and an initial value-choosing strategy to perform MLE calculation.

Binary:

1. source code: v-0.0.1-src
2. Linux X64: v-0.0.1-linux64-gcc7
3. Mac OSX ARM: v-0.0.1-OSX-M1
4. OSX X86: v-0.0.1-OSX-Intel
5. Windows: v-0.0.1-Window-X64

Note: for Windows user, one should install: Rtools42 and run C:\rtools42\ucrt64.exe, and in the bash, run

# to where you download pmat
cd pmat
cd ./release/Win64
tar vxf metilene-0.1-win64-rtools42.tar.gz
./metilene --help