This function performs unsupervised PCA on each mixscape class separately and projects each subspace onto all cells in the data.
Usage
PrepLDA(
object,
de.assay = "RNA",
pc.assay = "PRTB",
labels = "gene",
nt.label = "NT",
npcs = 10,
verbose = TRUE,
logfc.threshold = 0.25
)Arguments
- object
An object of class Seurat.
- de.assay
Assay to use for selection of DE genes.
- pc.assay
Assay to use for running Principle components analysis.
- labels
Meta data column with target gene class labels.
- nt.label
Name of non-targeting cell class.
- npcs
Number of principle components to use.
- verbose
Print progress bar.
- logfc.threshold
Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25. Increasing logfc.threshold speeds up the function, but can miss weaker signals.