centDHSbloodDMC.m {EpiDISH} | R Documentation |
Reference-based cell proportions estimation algorithms rely on a prior defined reference matrix. We leveraged cell-type specific DNAse Hypersensitive Site (DHS) information from the NIH Epigenomics Roadmap, and used 450k purified blood cell types dataset from Reinius et al (2012) to construct this improved reference DNA methylation dataset, as described in Teschendorff et al (2017). It contains 333 tsDHS-DMCs of 8 blood cell subtypes(You can select the corresponding cell types existing in the dataset, which you would like to estimate cell proportions, to use. Notice that Granulocytes consist of Neutrophils and Eosinophils. So you should include either of Granulocytes column or Neutrophils and Eosinophils columns.):
data(centDHSbloodDMC.m)
A matrix with 333 rows and 8 columns
B-cells
CD4+ T-cells
CD8+ T-cells
NK-cells
Monocytes
Neutrophils
Eosinophils
Granulocytes
Teschendorff AE, Breeze CE, Zheng SC, Beck S. A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. BMC Bioinformatics (2017) 18: 105. doi: 10.1186/s12859-017-1511-5.
Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlen S-E, Greco D, Soderhall C, Scheynius A, Kere J. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS ONE (2012) 7: e41361. doi: 10.1371/journal.pone.0041361.