centDHSbloodDMC.m: Whole blood reference of 333 tsDHS-DMCs and 7 blood cell...

In EpiDISH: Epigenetic Dissection of Intra-Sample-Heterogeneity

Description

Reference-based cell-type fraction 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 whole blood reference DNA methylation dataset, as described in Teschendorff et al (2017). It contains 333 tsDHS-DMCs of 7 blood cell subtypes(As the fractions of eosinophils are usually small, you could add the estimated fractions of neutrophils and eosinophils togetther as the estimations of granulocytes.):

Usage

data(centDHSbloodDMC.m)

Format

A matrix with 333 rows and 7 columns

Details

• B-cells

• CD4+ T-cells

• CD8+ T-cells

• NK-cells

• Monocytes

• Neutrophils

• Eosinophils

References

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.

EpiDISH documentation built on Nov. 8, 2020, 6:52 p.m.