Description Usage Arguments Value
This function will predict expression or cell embeddings from its k nearest neighbors index. For each cell, it will average its k neighbors value to get its new imputed value. It can average expression value in assays and cell embeddings from dimensional reductions.
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object |
The object used to calculate knn |
nn.idx |
k near neighbour indices. A cells x k matrix. |
assay |
Assay used for prediction |
reduction |
Cell embedding of the reduction used for prediction |
dims |
Number of dimensions of cell embedding |
return.assay |
Return an assay or a predicted matrix |
slot |
slot used for prediction |
features |
features used for prediction |
mean.function |
the function used to calculate row mean |
seed |
Sets the random seed to check if the nearest neighbor is query cell |
verbose |
Print progress |
return an assay containing predicted expression value in the data slot
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