HandleBiologicalZeros: 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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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


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