RunSingleR: generate SingleR object

In bimberlabinternal/OOSAP: OHSU-ONPRC Single-cell Analysis Package

Description

Compute SingleR classification on a Seurat object

Usage

RunSingleR(
  seuratObj = NULL,
  datasets = c("hpca", "blueprint", "dice", "monaco"),
  assay = NULL,
  resultTableFile = NULL,
  singlerSavePrefix = NULL,
  minFraction = 0.01,
  showHeatmap = TRUE,
  maxCellsForHeatmap = 20000
)

Arguments

seuratObj	A Seurat object
datasets	One or more datasets to use as a reference. Allowable values are: hpca, blueprint, dice, monaco, and immgen. See cellDex package for available datasets.
assay	The assay in the seurat object to use
resultTableFile	If provided, a table of results will be saved here
singlerSavePrefix	If provided, the SingleR results will be saved to RDS here
minFraction	If provided, any labels present with fraction of this or fewer across cells will be converted to Unknown
showHeatmap	If true, heatmaps will be generated showing the SingleR calls
maxCellsForHeatmap	The heatmap will only be plotted if the total cells is below this number

Value

The modified seurat object

bimberlabinternal/OOSAP documentation built on Jan. 19, 2021, 2:47 a.m.