PrepLDA | R Documentation |
This function performs unsupervised PCA on each mixscape class separately and projects each subspace onto all cells in the data.
PrepLDA(
object,
de.assay = "RNA",
pc.assay = "PRTB",
labels = "gene",
nt.label = "NT",
npcs = 10,
verbose = TRUE,
logfc.threshold = 0.25
)
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. |
Returns a list of the first 10 PCs from each projection.
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