Predicts cell classes for a new dataset based on trained model(s)
scPredict( new, reference, threshold = 0.55, max.iter.harmony = 20, recompute_alignment = TRUE, seed = 66 )
new | A seurat object containing cells to be classified |
---|---|
reference | A |
threshold | Threshold used for probabilities to classify cells into classes. All cells below
this threshold value will be labels as "unassigned". In the case of binary classification (two cell tyoes),
a threshold of |
max.iter.harmony | Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step. |
recompute_alignment | Recompute alignment? Useful if |
seed | Numeric seed for harmony |
A Seurat object with additional metadata columns with prediction probabilities associated to each class, a prediction
column,
indicating the classification based on the provided threshold and a generic_class
column without "unassigned" labels. Additionally,
two new reductions are returned:
scpred
: Aligned data using harmony
scpred_projection
: Raw projection using reference loadings
José Alquicira Hernández