get_var_genes: Get variable genes
In marcalva/diem: Debris-Containing Droplet Identification using EM

get_var_genes

R Documentation

Get variable genes

Description

This function finds the variable genes in an SCE object. The means and variances of the genes are calculated from the raw counts of the cluster set. Then, the means and variances are log-transformed after adding a constant of 1. A loess regression line is fit between the log counts and log variance, and the only top genes ranked by residual are variable genes used to initialize the clusters. The number of genes is specified with n_genes. The span for the loess function is given by lss (default is 0.3).

Usage

get_var_genes(x, n_genes = 2000, lss = 0.3, droplets.use = NULL,
  threads = 1, verbose = FALSE)

Arguments

`x`	An SCE object.
`n_genes`	Number of variable genes to return.
`lss`	Numeric value of the span parameter of the loess regression.
`droplets.use`	Vector of droplet IDs to use for getting variable genes. Default is to use the test set.
`threads`	Number of threads for parallel execution. Default is 1.
`verbose`	Verbosity.