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The methylation intensity, mCG, was calculated at each CpG location as (# methylated reads)/(# methylated reads + # unmethylated reads).
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Everything was calculated".
Most definitely was calculated.
For each CpG, the percentage of converted and unconverted Cs across all reads was calculated (%mCG).
A dosage of 8-MOP was calculated based on the volume of buffy coat collected using the following formula: treatment volume collected × 0.017 = mL of 8-MOP (20 mcg /mL).
The 100% reference value differs per column as percentages were calculated for mCs being part of mCGs according to the following equation: (Ʃ mCG/Ʃ (mCG + CG)) × 100 = % mCs of CGs.
Fractional methylation values were calculated for each CpG site as mCG/CGall, where mCG is the number of reads with a methylated cytosine at a CpG site (according to nonconversion) and CGall is the total number of reads mapped to the site.
Thus, fractional methylation levels were calculated as mCG/CG for each CpG, defined as the number of reads with methylated cytosines divided by the total number of reads mapped to the given CpG.
Once an approximate starting dose is calculated, round up or down to the available patch strength (25 mcg/hr, 50 mcg/hr, 75 mcg/hr, 100 mcg/hr) based on the clinical status of the patient.
Methylation broadness measures the fraction of cytosine sites detected as methylated in a given DNA segment, which is calculated as the proportion of methylated sites over the total sites in a sequence (termed as mCG/CG) [ 17].
A standard antibacterial agent (amikacin 30 mcg) was included in each assay as positive control.
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