Description Usage Arguments Details Value
View source: R/BiologicalZeros.R
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
1 2 3 4 | 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)
|
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
|
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' |
prob.mat |
matrix with same dimensions as |
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.
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
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