centDHSbloodDMC.m: Whole blood reference of 333 tsDHS-DMCs and 7 blood cell...
In sjczheng/EpiDISH: Epigenetic Dissection of Intra-Sample-Heterogeneity
centDHSbloodDMC.m R Documentation
Whole blood reference of 333 tsDHS-DMCs and 7 blood cell subtypes
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.
sjczheng/EpiDISH documentation built on Nov. 16, 2024, 11:54 a.m.
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| centDHSbloodDMC.m | R Documentation |
Whole blood reference of 333 tsDHS-DMCs and 7 blood cell subtypes
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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