Tsisal {TOAST} | R Documentation

## Complete Deconvolution of DNA methylation data based on TOAST and SISAL

### Description

A function to conduct complete reference-free deconvolution on DNA methylation data. If a full reference or a partial reference panel is provided, this function also automatically annotate the solved proportions to known cell types.

### Usage

    Tsisal(Y_raw, K = NULL, knowRef = NULL, possibleCellNumber = 3:15)

### Arguments

`Y_raw` | The DNA methylation 450K array data from complex tissues, rows for CpG sites and columns for samples.
`K` | The number of pure cell types, we allow users to pre-specify or use our method to estimate.
`knowRef` | The external reference panel for cell type label assignment.
`possibleCellNumber` | Range of possible number of cell types. Default is 3:15.

### Value

`estProp` | Estimated proportions.
`selMarker` | Selected cell type-specific markers.
`K` | Optional number of cell types.

### Author(s)

Weiwei Zhang <wwzhangly@163.com>

### References

Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. Weiwei Zhang, Hao Wu and Ziyi Li.

### Examples

    ### generate a simulation data
    knowRef <- matrix(runif(5000*5), 5000, 5)
    colnames(knowRef) <- paste0("CellType", 1:5)
    Y_raw <- matrix(runif(5000*20), 5000, 20)
    rownames(Y_raw) <- paste0("CpG", 1:5000)
    colnames(Y_raw) <- paste0("Sample", 1:20)

    Tsisal(Y_raw = Y_raw, K = 5, knowRef = knowRef)

    ## if cell type number is unknown
    # Tsisal(Y.raw = Y_raw, K = NULL, knowRef = knowRef, possibleCellNumber = 4:10)

[Package TOAST version 1.4.0 Index]