# Tools for the analysis of heterogeneous tissues

## Documentation for package ‘TOAST’ version 1.25.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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