Hi, I am interested in using some methylation data. The values are normalized between 0 and 1. However,I couldn’t an annotion showing how the normalization was done? I want to know how the methylation data is normalized between 0 and 1. Thanks!
The methylation value for a given gene is calculated by taking a weighted average of the methylation ratios of all CpG sites that are within 1000 bp from the gene’s TSS. The methylation ratio of each CpG site is defined as the number of reads where that CpG was methylated over the total number of reads covering that CpG. The weights of each CpG are calculated by the total number of reads covering that CpG overall the total number of reads covering any CpG within 1000 bp of the gene’s TSS. Let me know if this is clear.