findDiffAbundantMarkers: Find markers for differential abundant subpopulation

In altairwei/rhapsodykit: A Set of Tools for BD Rhapsody WTA Downstream Analysis

Find markers for differential abundant subpopulation

Description

Find markers for differential abundant subpopulation

Usage

findDiffAbundantMarkers(
  obj,
  da,
  method = c("COSG", "Seurat", "STG"),
  top_n = NULL,
  return_raw = FALSE,
  GPU = "",
  ...
)

Arguments

obj	Seurat object
da	DAseq results
method	Which method should be used to find markers. Method COSG is based on cosg, Seruat is based on SeuratMarkerFinder and STG is baed on STGmarkerFinder which requires python environment.
top_n	Return the top N markers from results. The order of markers is determined by scores for COSG and by average log2FC then P value for Seurat and STG.
return_raw	Return raw results produced by specified method.
GPU	Which GPU to use (GPU IDs), default using CPU. Note: this value will be used to set CUDA_VISIBLE_DEVICES environment.
...	Additional arguments passed to marker finder.

Value

A list of marker genes

altairwei/rhapsodykit documentation built on Feb. 1, 2023, 8:52 a.m.