computeLatentSpace: Computes the latent space of the expression matrix using PCA

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

Computes the latent space of the expression matrix using PCA

Description

Computes the latent space of the expression matrix using PCA

Usage

computeLatentSpace(
  object,
  projection_genes = NULL,
  filterThreshold = 0.05,
  filterNumMad = 2,
  projection_genes_method = NULL,
  num_PCs = 30,
  perm_wPCA = NULL
)

Arguments

object	the VISION object for which compute the latent space
projection_genes	character vector of gene names to use for PCA
filterThreshold	Threshold to apply when using the 'threshold' or 'fano' projection genes filter. If greater than 1, this specifies the number of cells in which a gene must be detected for it to be used when computing PCA. If less than 1, this instead specifies the proportion of cells needed
filterNumMad	Number of median absolute deviations to use when selecting highly-variable genes in each mean-sorted bin of genes
projection_genes_method	name of filtering method. Either 'threshold' or 'fano'(default)
num_PCs	the number of principal components to retain
perm_wPCA	If TRUE, apply permutation wPCA to determine significant number of components. Default is FALSE.

Value

the VISION with @latentSpace slot populated

YosefLab/VISION documentation built on June 14, 2024, 5:27 p.m.