CMEntdata

Data package providing example DNA methylation files used in the CMEnt vignette and examples. Includes: - A 450K microarray dataset on AML, originally provided in GEO with GSE63409 series identifier: - Preprocessed beta values, in gzip tsv format (GSE63409_beta_values.tsv.gz) - Samplesheet (GSE63409_samplesheet.tsv) - A mermaid file including the preprocessing steps having taken place (GSE63409_preprocessing.mmd) - An EPIC microarray dataset on PDAC, originally provided in GEO with GSE244696 series identifier, and reported differential methylation results reported in the accomodating publication: - Preprocessed beta values, in gzip tsv format (GSE244696_beta_values.tsv.gz) - Samplesheet (GSE244696_samplesheet.tsv) - Originally reported DMPs (GSE244696_DMPs.xlsx) - Originally reported DMRs (GSE244696_DMRs.xlsx) - A mermaid file including the preprocessing steps having taken place (GSE244696_preprocessing.mmd) - A simulated microarray dataset, based on the GEO series with identifier GSE40279, comprising of healthy blood from 656 healthy individuals, which was subset, after quantile preprocessing and probe filtering, to 100 samples and chromosomes 20 and 21, was residualized based on age and predicted sex, and had 500 DMRs spiked-in using CMEnt::simulateDMRs. - Simulated beta values subset, in gzip tsv format (GSE40279_sim_beta_values.tsv.gz) - Samplesheet (GSE40279_sim_samplesheet.tsv) - Spiked-in DMRs ground truth (GSE40279_sim_dmrs.tsv) - A mermaid file including the preprocessing steps having taken place (GSE40279_sim_preprocessing.mmd)- A simulated ONT dataset, based on an in-house dataset of 5 samples from neuroendocrine islets, augmented to 20 samples using CMEnt::augmentBSSeq, subset to chromosomes 20 and 21, and with 1000 DMRs spiked in using CMEnt::simulateDMRs, with max delta beta (delta_max) set to 0.3 and expected within-dmr correlation (expected_corr) set to 0.7. - Simulated bsseq binary file (ont_sim_bs.rds) - Sampleheet (ont_sim_samplesheet.tsv) - Spiked-in DMRs ground truth (ont_sim_dmrs.tsv) - A mermaid file including the preprocessing steps having taken place (ont_sim_preprocessing.mmd) The preprocessing scripts, metadata harmonization, and derived processed data files generated by the CMEnt authors are released under CC BY 4.0. The original raw GEO data and metadata remain attributable to their original GEO submitters and associated publications. Users should cite both this Zenodo record and the original GEO accession/publication when reusing the files.