Run Linear Discriminant Analysis

Run Linear Discriminant Analysis

Function to perform Linear Discriminant Analysis.

Usage

RunLDA(object, ...)

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

# S3 method for class '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 class '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