HandleBiologicalZeros {ADImpute} | R Documentation

## Get dropout probabilities

### Description

`GetDropoutProbabilities` computes dropout probabilities (probability of being a dropout that should be imputed rather than a true biological zero) using an adaptation of scImpute's approach

### Usage

    HandleBiologicalZeros(data, imputed, thre = 0.5, cell.clusters,
    labels = NULL, type = 'count', cores = BiocParallel::bpworkers(BPPARAM),
    BPPARAM = BiocParallel::SnowParam(type = "SOCK"),
    genelen = ADImpute::transcript_length, prob.mat = NULL)

### Arguments

`data` | matrix; original data before imputation
`imputed` | list; imputation results for considered methods
`thre` | numeric; between 0 and 1 specifying the threshold to determine dropout values
`cell.clusters` | integer; number of cell subpopulations
`labels` | character; vector specifying the cell type of each column of `data`
`type` | A character specifying the type of values in the expression matrix. Can be 'count' or 'TPM'
`cores` | integer; number of cores used for paralell computation
`BPPARAM` | parallel back-end to be used during parallel computation. See `BiocParallelParam-class`.
`genelen` | matrix with at least 2 columns: 'hgnc_symbol' and 'transcript_length'
`prob.mat` | matrix with same dimensions as `data` containing the dropout probabilities for the corresponding entries

### Details

This function follows scImpute's model to distinguish between true biological zeros and dropouts, and is based on adapted code from the scImpute R package.

### Value

list with 2 components: `zerofiltered`, a list equivalent to `imputed` but with entries of imputed likely biological zeros set back to zero, and `dropoutprobabilities` matrix with same dimensions as `data` containing the dropout probabilities for the corresponding entries

[Package ADImpute version 1.2.0 Index]