Classify {CHETAH} | R Documentation

## (Re)classify after running `CHETAHclassifier` using a confidence threshold
NOTE: In case of bulk reference profiles: only the correlations will be used, as the data does not allow for profile or confidence scores to be calculated.

### Description

(Re)classify after running `CHETAHclassifier` using a confidence threshold
NOTE: In case of bulk reference profiles: only the correlations will be used, as the data does not allow for profile or confidence scores to be calculated.

### Usage

    Classify(input, thresh = 0.1, return_clas = FALSE)

### Arguments

`input` | a SingleCellExperiment on which `CHETAHclassifier` has been run
`thresh` | a confidence threshold between -0 and 2. Selecting 0 will classify all cells, whereas 2 will result i n (almost) no cells to be classified. recommended: between 0.1 (fairly confident) and 1 (very confident)
`return_clas` | Instead of returning the SingleCellExperiment, only return the classification vector

### Value

a charachter vector of the cell types with the names of the cells

### Examples

    ## Classify all cells
    input_mel <- Classify(input_mel, 0)

    ## Classify only cells with a very high confidence
    input_mel <- Classify(input_mel, 1)

    ## Back to the default
    input_mel <- Classify(input_mel)

    ## Return only the classification vector
    input_mel <- Classify(input_mel, 1, return_clas = TRUE)

[Package CHETAH version 1.0.5 Index]