ExtractGenes: Extracts common set of genes across all datasets

In quon-titative-biology/scAlign: An alignment and integration method for single cell genomics

Description

Extracts common set of genes across all datasets

Usage

ExtractGenes(seurat.obj1, seurat.obj2 = NULL)

Arguments

seurat.obj1	Either a preprocessed Seurat object or a list of Seurat objects
seurat.obj2	A preprocessed Seurat object (optional, for simple binary conditions)

Value

A character vector of gene names which exhibit varible expression across all datasets

See Also

as.SingleCellExperimentList

SelectColors

DecoderVariance

MeanDecoderVariance

GetCharMetadata

Examples

for (i in 1:length(seurat.list)) {
  seurat.list[[i]] <- NormalizeData(seurat.list[[i]])
  seurat.list[[i]] <- ScaleData(seurat.list[[i]], do.scale=T, do.center=T, display.progress=T)
  seurat.list[[i]] <- FindVariableFeatures(seurat.list[[i]], nFeatures = 3000)
}
genes.use <- ExtractGenes(seurat.list)

quon-titative-biology/scAlign documentation built on Nov. 17, 2021, 9:57 a.m.