FindClustersAndDimRedux: FindClustersAndDimRedux

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

Description

FindClustersAndDimRedux

Usage

FindClustersAndDimRedux(
  seuratObj,
  dimsToUse = NULL,
  saveFile = NULL,
  forceReCalc = F,
  minDimsToUse = NULL,
  umap.method = "umap-learn",
  UMAP_NumNeib = 40L,
  UMAP_MinDist = 0.2,
  UMAP_Seed = 1234,
  UMAP.NumEpoc = 500,
  maxTsneIter = 10000,
  tSNE_perplexity = 30,
  clusterResSet = c(0.2, 0.4, 0.6, 0.8, 1.2)
)

Arguments

seuratObj,	A Seurat object.
dimsToUse	The number of dims to use. If null, this will be inferred using FindSeuratElbow()
saveFile	If provided, the seurat object will be saved as RDS to this location
forceReCalc	If true, all steps will be performed even if already marked complete
minDimsToUse	The minimum numbers of dims to use. If dimsToUse is provided, this will override.
umap.method	The UMAP method, either uwot or umap-learn, passed directly to Seurat::RunUMAP
maxTsneIter	The value of max_iter to provide to RunTSNE. Increasing can help large datasets.
tSNE_perplexity	tSNE perplexity. Passed directly to Seurat::RunTSNE(), but OOSAP:::.InferPerplexityFromSeuratObj() corrects it if need be based dataset dims.
clusterResSet	a vector of clustering resolutions, default is (0.2, 0.4, 0.6, 0.8, 1.2).

Value

A modified Seurat object.

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