Select variable genes — selectVariableFeatures • SRTpipeline

Select variable genes

selectVariableFeatures(
  SRTProj,
  nfeatures = 2000,
  type = c("HVGs", "SVGs"),
  method = "vst",
  use_custom_features = NULL,
  exclude_features = NULL
)

Arguments

SRTProj: a SRTProject object.
nfeatures: a positive integer, the number of variable features to be chosen.
type: a string, one of "HVGs" and "SVGs", represent the type of variable genes to be chosen.
method: a string, the method to use, including 'vst' if type='HVGs', "SPARK-X" if type='SVGs'.
use_custom_features: a string vector, a group of custom genes to use. If this argument is not NULL, it will use this group of custom genes as variable genes.
exclude_features: a string vector, a group of genes to be excluded when finding variable genes.

Value

a revised SRTProject object.