r-watermelon 2.12.0
Illumina 450 methylation array normalization and metrics
The standard index of DNA methylation (beta) is computed from methylated and unmethylated signal intensities. Betas calculated from raw signal intensities perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. This package provides 15 flavours of betas and three performance metrics, with methods for objects produced by the methylumi and minfi packages.
- Outputs:
out - Website: https://bioconductor.org/packages/wateRmelon/
- Licenses: GPL 3
- Package source: gnu/packages/bioconductor.scm
- Builds: See build status
- Issues: See known issues
Installation
Install r-watermelon 2.12.0 as follows:
guix install r-watermelon@2.12.0
Or install the latest version:
guix install r-watermelon
You can also install packages in augmented, pure or containerized environments for development or simply to try them out without polluting your user profile. See the guix shell documentation for more information.