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

Description Usage Arguments Value

View source: R/AnalysisFunctions.R

Description

Computes the latent space of the expression matrix using PCA

Usage

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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 Sept. 14, 2021, 5:27 p.m.