Ser2Monocle_MakeNProcess: Ser2Monocle_MakeNProcess

In eisascience/scCustFx: single-cell custom fxs Package

Ser2Monocle_MakeNProcess

Description

Performs the preprocessing steps for single-cell RNA-seq data using Monocle 2 package

Usage

Ser2Monocle_MakeNProcess(
  SeurObj = NULL,
  retunMon = T,
  PCAnDim = 20,
  doUMAP = T,
  min_dist = 0.3,
  n_neighbors = 40,
  dotSNE = F,
  doClust = T,
  ClusLouvRes = 5e-05,
  louvain_iter = 3,
  KeepTopNgenes = 3000,
  minExprGeneDet = 0.1,
  upperScale = 2,
  lowerScale = 2.5,
  assay = NULL
)

Arguments

SeurObj	A Seurat object with a count matrix and metadata
retunMon	Logical value indicating whether to return the Monocle 2 object (default = TRUE)
PCAnDim	Number of principal components to retain for dimensionality reduction (default = 20)
doUMAP	Logical value indicating whether to perform UMAP reduction (default = TRUE)
min_dist	The effective minimum distance between embedded points in the UMAP plot (default = 0.3)
n_neighbors	The size of local neighborhood (default = 40)
dotSNE	Logical value indicating whether to perform tSNE reduction (default = FALSE)
doClust	Logical value indicating whether to perform clustering (default = TRUE)
ClusLouvRes	Louvain resolution parameter for clustering (default = 0.00005)
louvain_iter	The number of iterations for the Louvain algorithm (default = 3)
KeepTopNgenes	The number of top variable genes to use in the analysis (default = 3000)
minExprGeneDet	The minimum expression threshold for genes to be considered expressed (default = 0.1)
upperScale	The scaling factor for the upper bound for filtering cells by total mRNA expression (default = 2)
lowerScale	The scaling factor for the lower bound for filtering cells by total mRNA expression (default = 2.5)
assay	The assay type to use (default = NULL)

Value

A Monocle object

Examples

data("pbmc_small")
pbmc_small <- as.Seurat(pbmc_small)
SeurObj_cds <- Ser2Monocle_MakeNProcess(SeurObj = pbmc_small, retunMon = T,
PCAnDim = 20, doUMAP = T, min_dist=.3,
n_neighbors = 40, dotSNE = F, doClust = T,
ClusLouvRes = 0.00005, louvain_iter = 3,
KeepTopNgenes = 3000, minExprGeneDet = 0.1,
upperScale = 2, lowerScale = 2.5, assay = NULL)

eisascience/scCustFx documentation built on June 2, 2025, 3:59 a.m.