GetDropoutProbabilities {ADImpute} | R Documentation |
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
GetDropoutProbabilities(data, thre, cell.clusters, labels = NULL, type = 'count', cores, BPPARAM, genelen = ADImpute::transcript_length)
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
|
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 |
genelen |
matrix with at least 2 columns: 'hgnc_symbol' and 'transcript_length' |
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.
matrix with same dimensions as data
containing the dropout
probabilities for the corresponding entries