get_SmoothByBin_PseudotimeExp: Smooth cells into bins based on pseudotime or State

In jiang-junyao/IReNA: IReNA

Smooth cells into bins based on pseudotime or State

Description

Divide cells into bins across pseudotime and return expression profile

Usage

get_SmoothByBin_PseudotimeExp(
  seurat_object,
  FC = TRUE,
  Bin = 50,
  method = "Pseudotime",
  FcType = "Q95"
)

Arguments

seurat_object	seurat object, where meta.data should contain Pseudotime
FC	logic, indicating whether to add FoldChangeQ95 to the first column, default is TRUE
Bin	numeric, indicating the numbers of bins which divide the pseudotime, default is 50
method	'Pseudotime' or 'State'. Pseudotime method firstly orders all cells according to pseudotime, and then smooth these cells into ‘Bin' number of bins. State method firstly orders all cells according to pseudotime, and then smooth cells in each state into ('Bin'/number of state) number of bins.
FcType	'Q95' or 'Q90', FoldChange threshold, default is 'Q95'

Value

return a expression profile

Examples

load(system.file("extdata", "test_seurat.rda", package = "IReNA"))
monocle_object = get_pseudotime(test_seurat)
seurat_object_pseudotime=add_pseudotime(seurat_object = test_seurat,monocle_object = monocle_object)
get_SmoothByBin_PseudotimeExp(seurat_object_pseudotime, Bin = 50, FcType = "Q95")

jiang-junyao/IReNA documentation built on May 2, 2024, 6:54 a.m.