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.
Usage
PredictAssay(
object,
nn.idx,
assay,
reduction = NULL,
dims = NULL,
return.assay = TRUE,
slot = "scale.data",
features = NULL,
mean.function = rowMeans,
seed = 4273,
verbose = TRUE
)Arguments
- object
The object used to calculate knn
- nn.idx
k near neighbor 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