This function performs imputation on a Seurat object using various methods including ALRA, MAGIC, etc. The imputed values are stored as a new assay in the Seurat object.
Usage
RunImputation(
srt,
assay = NULL,
slot = "data",
method = c("alra", "magic", "knn_smooth"),
new_assay = NULL,
features = NULL,
verbose = TRUE
)Arguments
- srt
An object of class Seurat.
- assay
Name of assay to use for imputation.
- slot
Name of slot to use for imputation (default: "data").
- method
Imputation method to use. One of "alra", "magic", "knn_smooth".
- new_assay
Name of the new assay to store imputed data (default: paste0(method, "_imputed")).
- features
Features to use for imputation. If NULL, uses variable features.
- verbose
Print progress messages.