FindVariableFeatures.STACAS: FindVariableFeatures.STACAS

In carmonalab/STACAS: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat

FindVariableFeatures.STACAS

Description

Select highly variable genes (HVG) from an expression matrix. Genes from a blocklist (e.g. cell cycling genes, mitochondrial genes) can be excluded from the list of variable genes, as well as genes with very low or very high average expression

Usage

## S3 method for class 'STACAS'
FindVariableFeatures(
  obj,
  nfeat = 1500,
  genesBlockList = "default",
  min.exp = 0.01,
  max.exp = 3
)

Arguments

obj	A Seurat object containing an expression matrix
nfeat	Number of top HVG to be returned
min.exp	Minimum average normalized expression for HVG. If lower, the gene will be excluded
max.exp	Maximum average normalized expression for HVG. If higher, the gene will be excluded
genesBlocklist	Optionally takes a list of vectors of gene names. These genes will be removed from initial HVG set. If set to "default", STACAS uses its internal list data("genes.blocklist"). This is useful to mitigate effect of genes associated with technical artifacts or batch effects (e.g. mitochondrial, heat-shock response). If set to 'NULL' no genes will be excluded

Value

Returns a list of highly variable genes

carmonalab/STACAS documentation built on Feb. 3, 2024, 7:42 a.m.