PreprocessSubsetData: A wrapper for preprocessing subsetted Seurat object

In crazyhottommy/scclusteval: Evaluate the single cell clustering

Description

The wrapper does FindVeriableGenes, ScaleData, RunPCA, JackStraw to determine how many PCs to use, ProjectPCA and FindClusters and retrun a fully processed Seurat object. The input subsetted seurat object is supposed to be fully processed as well. So the NormalizeData step is not necessary.

Usage

PreprocessSubsetData(
  object,
  variable.features.n = 3000,
  num.pc = 20,
  pc.use = NULL,
  workers = 2,
  score.thresh = 1e-05,
  sig.pc.thresh = 0.05,
  n.start = 100,
  nn.eps = 0,
  resolution = 0.8,
  k.param = 30,
  ...
)

Arguments

object	A subsetted Seurat object created by RandomSubsetData
variable.features.n	number of variable features for SCTransform
num.pc	number of PCs to calculate in RunPCA, JackStraw and JackStrawPlot step. The optimal PCs for FindClusters will be determined by only significant PCs from JackStrawPlot or if pc.use is set, JackStraw step will be skipped and use pc.use for FindClusters.
pc.use	number of PCs used for FindClusters. if pc.use is set, JackStraw step will be skipped and use pc.use for FindClusters. score.thresh and sig.pc.thresh will be ignored.
workers	number of CPUs to use for plan parallel processing
score.thresh	Threshold to use for the proportion test of PC significance.
sig.pc.thresh	Threshold for the significance of a particular PC.
n.start	Number of random start.
nn.eps	Error bound when performing nearest neighbor seach using RANN; default of 0.0 implies exact nearest neighbor search. See FindClusters.
resolution	Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities. see FIndClusters.
k.param	Defines k for the k-nearest neighbor algorithm.
...	any other parameters

Value

a fully processed Seurat object

Examples

## Not run: 
pbmc_small_subset<- RandomSubsetData(pbmc_small, 0.8)
pbmc_small_subset_processed<- PreprocessSubsetData(pbmc_small_subset)
[e-mail]

## End(Not run)

crazyhottommy/scclusteval documentation built on Aug. 5, 2021, 3:20 p.m.