uddin-research-group-at-usf/CICPT_1831_Rwanda

Leukocyte methylomic imprints of exposure to the genocide against the Tutsi in Rwanda: a pilot epigenome-wide analysis # CICPT_1831_Rwanda 1. Prior to any analysis, test is done to check if samples are put on desired plates and chips. For this test, samples sheet prepared to run chips will be compared with the sample sheet of the output data (after running chips). Run `samples_on_plates_check.R` file. All the samples need to be at desired locations as per input sample sheet. 2. Discordant sex check need to be done to check if the gender on input sample sheet matched with the data generated. Run `Disccordant_Sex_check.R`. There should be not discordant sex and if exists then problematic samples need to be removed from the analysis. 3. Cross-hybridizing probes file which is used for quality control to remove the probes can be prepared by running `MkCrossHybridData.R`. The cross hybrid probe files are download from internet for epic chips. 4. Run `PreprocessNoob.R` for preprocessing using `Noob` method. 5. Quality control test can be performed by running `Quality_control_RawandaEWAS.R`. This will try to remove the missing values, perform normalization and plot density plots. 6. For PCA to find the variation in the data run `Combat_PCA.R`. This is done to remove batch effects. 7. To run analysis on pre-processed and quality controlled data, run `mcSEA_on_Top_variable_Probes_clean.R` file doi.org. 8. Use `Ridge_regression.R` to perform Ridge regression analysis. # Supplementary Files 1. Suplementary table 1 is referenced in our paper and available as a supplementary file. 2. During the review of our manuscript, we were asked to conduct DMR analyses on the full set of QC'd Epic data (818,720 probes). We found 233 DMRs in children and 1,111 DMRs in mothers. These have been provided as Supplementary Tables 2 and 3, respectively, but are not referenced directly in the paper itself.