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Added links for pre-defined regions that contain both genic and inter-genic regions
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dlukacso authored Oct 2, 2024
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Expand Up @@ -23,6 +23,8 @@ Assuming you have completed all pre-processing and normalization procedures, her
+ Inter-genic regions, 450k array: `extdata/450k_InterGene_3_200.rds`.Load this via `system.file("extdata", "450k_InterGene_3_200.rds", package = "coMethDMR", mustWork = TRUE)`
+ Genic regions, EPIC array: download the supplemental data file from <https://github.com/TransBioInfoLab/coMethDMR_data/blob/main/data/EPIC_10b4_Gene_3_200.rds>
+ Inter-genic regions, EPIC array: download the supplemental data file from <https://github.com/TransBioInfoLab/coMethDMR_data/blob/main/data/EPIC_10b4_InterGene_3_200.rds>
+ Both Genic and Inter-genic regions, 450k array: downlaod the supplemental data file [hg19 data](https://github.com/TransBioInfoLab/coMethDMR_data/blob/main/data/450k_All_3_200_hg19.rds) or [hg38 data](https://github.com/TransBioInfoLab/coMethDMR_data/blob/main/data/450k_All_3_200_hg38.rds)
+ Both Genic and Inter-genic regions, EPIC array: downlaod the supplemental data file [hg19 data](https://github.com/TransBioInfoLab/coMethDMR_data/blob/main/data/EPIC_10b4_All_3_200_hg19.rds) or [hg38 data](https://github.com/TransBioInfoLab/coMethDMR_data/blob/main/data/EPIC_10b4_All_3_200_hg38.rds)
3. **Adjust Methylation for Covariates** with the `GetResiduals()` function; your methylation values may be confounded by clinical variables unrelated to your treatment, such as sex, age, or even [the square of age](https://www.nature.com/articles/s41598-021-88504-0)
+ *Input*: your methylation data and covariates from **Step 1**
+ *Output*: a matrix of methylation residuals in *probe by sample* form
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