Run Linear Discriminant Analysis

Function to perform Linear Discriminant Analysis.

RunLDA(object, ...)

# S3 method for default
RunLDA(
  object,
  labels,
  assay = NULL,
  verbose = TRUE,
  ndims.print = 1:5,
  nfeatures.print = 30,
  reduction.key = "LDA_",
  seed = 42,
  ...
)

# S3 method for Assay
RunLDA(
  object,
  assay = NULL,
  labels,
  features = NULL,
  verbose = TRUE,
  ndims.print = 1:5,
  nfeatures.print = 30,
  reduction.key = "LDA_",
  seed = 42,
  ...
)

# S3 method for Seurat
RunLDA(
  object,
  assay = NULL,
  labels,
  features = NULL,
  reduction.name = "lda",
  reduction.key = "LDA_",
  seed = 42,
  verbose = TRUE,
  ndims.print = 1:5,
  nfeatures.print = 30,
  ...
)

Arguments

object: An object of class Seurat.
...: Arguments passed to other methods
labels: Meta data column with target gene class labels.
assay: Assay to use for performing Linear Discriminant Analysis (LDA).
verbose: Print the top genes associated with high/low loadings for the PCs
ndims.print: Number of LDA dimensions to print.
nfeatures.print: Number of features to print for each LDA component.
reduction.key: Reduction key name.
seed: Value for random seed
features: Features to compute LDA on
reduction.name: dimensional reduction name, lda by default