Tools for the analysis of heterogeneous tissues

Documentation for package ‘TOAST’ version 1.23.0

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