GetDropoutProbabilities: Get dropout probabilities

In beyergroup/ADImpute: Adaptive Dropout Imputer (ADImpute)

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

GetDropoutProbabilities(data, thre, cell.clusters, labels = NULL,
type = 'count', cores, BPPARAM, genelen = ADImpute::transcript_length)

Arguments

data	matrix; original data before imputation
thre	numeric; probability threshold to classify entries as biological zeros
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'

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

matrix with same dimensions as data containing the dropout probabilities for the corresponding entries

beyergroup/ADImpute documentation built on Dec. 19, 2021, 8:48 a.m.