Description Usage Arguments Value Examples
This function distinguishes zeros that are likely to be dropouts from those biologically true zeros based on pairwise Jaccard Index between cells.
1 2 3 4 5 6 7 8 | findDropouts(
exprs,
t = 0.2,
genes = NULL,
ncores = 1,
return_J = FALSE,
verbose = TRUE
)
|
exprs |
An input log-transformed data matrix. The rows and columns correspond to genes and cells, respectively. |
t |
Threshold (between 0 and 1) for determining similar cells. Default is 0.2. |
genes |
A vector containing gene symbols that will get imputed. Default is NULL, in which case all available genes in the matrix exprs will be imputed. |
ncores |
Number of cores to use. Default is 1. |
return_J |
Whether to return the calculated pairwise Jaccard matrix between cells. Default is FALSE. |
verbose |
Whether to show the progress of dropout identification. Default is TRUE. |
A list with the following components:
dropout_ind |
A matrix in which each row contains the indices of a dropout |
J |
(optional) Calculated pairwise Jaccard Index between cells |
1 2 3 4 5 6 | data(ge_10x_sample)
results1 <- findDropouts(ge_10x_sample, ncores = 2, return_J = TRUE)
# pairwise Jaccard Index between cells
J <- results1$J
# indices of identified dropouts
dropout_ind <- results1$dropout_ind
|
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