DNA methylation data of hematopoietic transplantation patients
Description
The analysis was performed to decide if the age of the recipient body affects epigenetic aging in the donor cells. All raw data was processed starting from .idat files with R for this analysis. Based on a recent study that compared different DNA methylation raw data processing pipelines for epigenetic clocks 3 we decided on using ENmix with the suggested optimal parameters for epigenetic clocks from the comparison: Out-of-bag background correction, RELIC dye-bias correction, quantile normalization separately for methylated and unmethylated intensities and RCP correction of probe design type bias. The folder with raw .idat files was first loaded with ENmix::readidat() then profiled by ENmix:qcinfo() with default settings. Loaded data was then sequentially applied to ENmix::preprocessENmix(), ENmix::norm.quantile() and ENmix::rcp() with the above described parameters. ENmix::qcfilter() was then applied, removing very low quality CpGs and samples detected by the qcinfo() function and imputing missing values. The result from this pipeline is a table of DNA methylation beta values. This pipeline was run separately for each batch of measurements. Included in this Mendeley Data collection is the processed and normalized (as described above) DNA methlation beta values for all samples. The batches are exported as separate files. The comRand.csv file contains a table where the "randID" column corresponds to columns in the batchX.csv files. This table also has all the required information about the ages of the donors and recipients of the hematopoietic transplantation (at time of transplantation) and the age of the measured cells at the time of measurement (column ageCells).
Files
Steps to reproduce
Described in the associated manuscript published in Aging Cell