Calc.Cor.Seurat: Calc.Cor.Seurat

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

Calc.Cor.Seurat

Description

Calculate gene correlation on a Seurat object.

Usage

Calc.Cor.Seurat(
  assay.use = "RNA",
  slot.use = "data",
  quantileX = 0.95,
  max.cells = 40000,
  seed = p$seed,
  digits = 2,
  obj = combined.obj
)

Arguments

assay.use	The assay to use from the Seurat object. Default: 'RNA'
slot.use	The slot to use from the assay in the Seurat object. Default: 'data'
quantileX	The quantile level for the calculation. Default: 0.95
max.cells	Maximum number of cells to be used in the calculation. Default: 40000
seed	The random seed used for the calculation. Default: p$seed
digits	The number of decimal places to round the correlation and covariance values. Default: 2
obj	The Seurat object to perform calculations on. Default: combined.obj

Examples

## Not run: 
if (interactive()) {
  combined.obj <- calc.q99.Expression.and.set.all.genes(combined.obj, quantileX = 0.99, max.cells = 400000, set.all.genes = FALSE)
  combined.obj <- Calc.Cor.Seurat(assay.use = "RNA", slot.use = "data", digits = 2, obj = combined.obj, quantile = 0.99, max.cells = 40000)
}

## End(Not run)

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