GetDropoutProbabilities: Get dropout probabilities

Description Usage Arguments Details Value

View source: R/BiologicalZeros.R

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

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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


ADImpute documentation built on Nov. 8, 2020, 5:30 p.m.