domains / families / science / cell-type-deconvolution

cell-type-deconvolution

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Estimates cell-type composition from bulk DNA methylation and uses it to defuse the single biggest EWAS confounder. Covers reference-based deconvolution (Houseman constrained-projection, minfi estimateCellCounts2 with FlowSorted.Blood.EPIC + IDOL-optimized libraries, EpiDISH RPC/CBS/CP, 12-cell extended, cord-blood nRBC references, EpiSCORE/hepidish for solid tissue), reference-free correction (ReFACTor, RefFreeEWAS, SVA), using fractions as covariates vs the compositionality/collinearity trap, and cell-type-resolved EWAS (CellDMC, TCA, TOAST, omicwas, HIRE). Use when estimating blood/tissue cell fractions, adjusting an EWAS for composition, choosing a deconvolution reference, or attributing a methylation signal to a cell type. For the EWAS confounder-vs-mediator decision see ewas-design; for the IEAA cell-count adjustment of DNAm age see epigenetic-clocks; for clean beta input see array-preprocessing.

When to use

• estimating blood/tissue cell fractions
• adjusting an EWAS for composition
• choosing a deconvolution reference
• attributing a methylation signal to a cell type
• reference-based deconvolution
• reference-free correction
• cell-type-resolved EWAS

When not to use

• EWAS confounder-vs-mediator decision
• IEAA cell-count adjustment of DNAm age
• clean beta input preprocessing
• single-cell/sorted atlases for reference building
• predictive-model training/leakage

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