Tools for the analysis of heterogeneous tissues

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Documentation for package ‘TOAST’ version 1.14.0

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assignCellType Align cell types when reference proportions are known
beta_emp Simulated methylation 450K array data with related
CBS_PBMC_array An example dataset for partial reference-free cell composition estimation from tissue gene expression
cedar Testing cell type specific differential signals for specified phenotype by considering DE/DM state corrleation between cell types.
ChooseMarker Choose cell type-specific markers from pure cell type profiles or single cell data
csDeconv Improve reference-free deconvolution using cross-cell type differential analysis
csTest Testing differential signals for specified phenotype and cell type(s).
DEVarSelect Feature selection for reference-free deconvolution using cross-cell type differential analysis
findRefinx findRefinx
fitModel Fit model with proportions and phenotypes.
GetPrior Get prior knowledge for supported tissue types
makeDesign Generate design matrix from input phenotypes and proportions.
MDeconv Estimate cell compoisitons via partial reference-free deconvolution.
myprojectMix Replicate the function myprojectMix() from RefFreeEWAS package
myRefFreeCellMix Replicate the function RefFreeCellMix() from RefFreeEWAS package
myRefFreeCellMixInitialize Replicate the function RefFreeCellMixInitialize() from RefFreeEWAS package
plotCorr Show DE/DM state correlation between cell types
RA_100samples An example dataset for cellular proportion estimation and multiple factor design
Tsisal Complete Deconvolution of DNA methylation data based on TOAST and SISAL