RunLDA: Run Linear Discriminant Analysis

In Seurat: Tools for Single Cell Genomics

Run Linear Discriminant Analysis

Description

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

Seurat documentation built on May 29, 2024, 4:20 a.m.