centBloodSub.m: Whole blood reference of 188 tsDHS-DMCs and 7 blood cell...
In EpiDISH: Epigenetic Dissection of Intra-Sample-Heterogeneity
Description
Usage
Format
Details
References
Description
This reference is a subset of centDHSbloodDMC.m, and contains 188
DMCs which exhibit similar median DNAm values across epithelial cells,
fibroblasts and ICs to ensure that the estimation of IC subtype fractions is
not confounded by the epithelial and fibroblast cells in the sample. It should
be used in the hepidish function to estimate fractions of immunce cell
subtypes.
Usage
1
Format
A matrix with 188 rows and 7 columns
Details
B-cells
CD4+ T-cells
CD8+ T-cells
NK-cells
Monocytes
Neutrophils
Eosinophils
References
Zheng SC, Webster AP, Dong D, Feber A, Graham DG, Sullivan R, Jevons S, Lovat LB,
Beck S, Widschwendter M, Teschendorff AE
A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix.
Epigenomics (2018) 10: 925-940.
doi:
10.2217/epi-2018-0037.
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.
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Description Usage Format Details References
Description
This reference is a subset of centDHSbloodDMC.m, and contains 188
DMCs which exhibit similar median DNAm values across epithelial cells,
fibroblasts and ICs to ensure that the estimation of IC subtype fractions is
not confounded by the epithelial and fibroblast cells in the sample. It should
be used in the hepidish function to estimate fractions of immunce cell
subtypes.
Usage
1 |
Format
A matrix with 188 rows and 7 columns
Details
B-cells
CD4+ T-cells
CD8+ T-cells
NK-cells
Monocytes
Neutrophils
Eosinophils
References
Zheng SC, Webster AP, Dong D, Feber A, Graham DG, Sullivan R, Jevons S, Lovat LB, Beck S, Widschwendter M, Teschendorff AE A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix. Epigenomics (2018) 10: 925-940. doi: 10.2217/epi-2018-0037.
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
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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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