BiSplit_DE: BiSplit_DE
In eisascience/scCustFx: single-cell custom fxs Package

BiSplit_DE

R Documentation

BiSplit_DE

Description

A function to perform differential expression analysis using BiSplit algorithm.

Usage

BiSplit_DE(
  SerObj,
  gate_feat = NULL,
  gate_thr = 0,
  plot_DimPlot = F,
  doDE = T,
  cols = c("gray", "red"),
  raster = F,
  assay = "RNA",
  layer = "data",
  only.pos = F,
  min.pct = 0.65,
  min.diff.pct = 0.2,
  logfc.threshold = 0.25
)

Arguments

`SerObj`	An object of class Seurat
`gate_feat`	A character vector of feature names to use as gatekeepers for the BiSplit algorithm.
`gate_thr`	The threshold value for the gatekeepers. Default is 0.
`plot_DimPlot`	Logical value indicating whether to generate a DimPlot of the results. Default is FALSE.
`doDE`	set doDE to F from T (default) when just visualizing the gating dimplot
`cols`	A character vector of colors to use for plotting the results. Default is c("gray", "red").
`raster`	Logical value indicating whether to rasterize the plot. Default is FALSE.
`assay`	The assay type to use for the analysis. Default is "RNA".
`layer`	The layer to use for the analysis. Default is "data".
`only.pos`	Logical value indicating whether to only consider positive differential expression. Default is FALSE.
`min.pct`	The minimum percentage of cells expressing a feature to consider it. Default is 0.65.
`min.diff.pct`	The minimum percentage difference in expression between groups to consider a feature differentially expressed. Default is 0.2.
`logfc.threshold`	The log-fold change threshold to use for identifying differentially expressed features. Default is 0.25.