centBloodSub.m: Whole blood reference of 188 tsDHS-DMCs and 7 blood cell...
In sjczheng/EpiDISH: Epigenetic Dissection of Intra-Sample-Heterogeneity
centBloodSub.m R Documentation
Whole blood reference of 188 tsDHS-DMCs and 7 blood cell subtypes
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
data(centBloodSub.m)
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.
sjczheng/EpiDISH documentation built on Nov. 13, 2022, 9:57 p.m.
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| centBloodSub.m | R Documentation |
Whole blood reference of 188 tsDHS-DMCs and 7 blood cell subtypes
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
data(centBloodSub.m)
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.
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