inferTissue {sesame} | R Documentation

## inferTissue1 infers the tissue of a single sample (as identified through the branchIDs in the row data of the reference) by reporting independent composition through cell type deconvolution.

### Description

inferTissue1 infers the tissue of a single sample (as identified through the branchIDs in the row data of the reference) by reporting independent composition through cell type deconvolution.

### Usage

    inferTissue(
      betas,
      reference = NULL,
      platform = NULL,
      abs_delta_beta_min = 0.3,
      auc_min = 0.99,
      coverage_min = 0.8,
      topN = 15
    )

### Arguments

`betas` | Named vector with probes and their corresponding beta value measurement
`reference` | Summarized Experiment with either hypomethylated or hypermethylated probe selection (row data), sample selection (column data), meta data, and the betas (assay)
`platform` | String representing the array type of the betas and reference
`abs_delta_beta_min` | Numerical value indicating the absolute minimum required delta beta for the probe selection criteria
`auc_min` | Numeric value corresponding to the minimum AUC value required for a probe to be considered
`coverage_min` | Numeric value corresponding to the minimum coverage requirement for a probe to be considered. Coverage is defined here as the proportion of samples without an NA value at a given probe.
`topN` | number of probes to at most use for each branch

### Value

inferred tissue as a string

### Examples

    sesameDataCache("MM285") # if not done yet
    sdf = sesameDataGet("MM285.1.SigDF")
    inferTissue(getBetas(dyeBiasNL(noob(sdf))))

[Package sesame version 1.12.9 Index]