computeProjectionGenes: filter data accourding to the provided filters

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

filter data accourding to the provided filters

Description

filter data accourding to the provided filters

Usage

computeProjectionGenes(
  object,
  threshold = NULL,
  num_mad = NULL,
  projection_genes_method = NULL,
  projection_genes = NULL
)

Arguments

object	the VISION object
threshold	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
num_mad	Number of median absolute deviations to use when selecting highly-variable genes in each mean-sorted bin of genes
projection_genes_method	a method to select genes either 'Threshold' or 'Fano'
projection_genes	a list of genes to use specifically. If this is supplied then 'projection_genes_method' is ignored

Value

the VISION object, populated with filtered data

YosefLab/VISION documentation built on Feb. 19, 2023, 9:50 p.m.