FindCorrelatedGenes: FindCorrelatedGenes

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

FindCorrelatedGenes

Description

Find correlated genes in a Seurat object

Usage

FindCorrelatedGenes(
  gene = "TOP2A",
  obj = combined.obj,
  assay = "RNA",
  slot = "data",
  HEonly = FALSE,
  minExpr = 1,
  minCells = 1000,
  trailingNgenes = 1000
)

Arguments

gene	Gene of interest. Default: 'TOP2A'
obj	Seurat object to find the correlated genes from. Default: combined.obj
assay	Assay to be used from the Seurat object. Default: 'RNA'
slot	Slot to be used from the specified assay in the Seurat object. Default: 'data'
HEonly	Logical, if TRUE, filters matrix to high-expressing genes only. Default: FALSE.
minExpr	Minimum expression level for a gene to be considered. Default: 1
minCells	Minimum number of cells expressing a gene for the gene to be considered. Default: 1000
trailingNgenes	Number of top genes to consider based on their correlation. Default: 1000

See Also

rowSums2

Examples

## Not run: 
if (interactive()) {
  FindCorrelatedGenes(gene = "TOP2A", obj = combined.obj)
  write_clip(names(head(topGenes[-(1:6)], n = 50)))
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.