Calculate heuristic metrics to determine optimal number of principal components for downstream analyses

Source: R/seurat_wrappers.R

Calculate heuristic metrics to determine optimal number of principal components for downstream analyses

CalcPCHeuristics(
  seurat.obj,
  reduction = "pca",
  store.name = "pca_metrics",
  percent.stdev.range = 0.05,
  set.pcs = NA,
  force_tp = FALSE
)

Arguments

seurat.obj

Seurat object
percent.stdev.range

Percent of PCA standard deviation range to use for
set.pcs

Number of PCs to use for maximum distance and derivative calculations
derivs.change.threshold

Threshold used for second derivative changes

Value

Returns object with optimal PC information within the object@misc slot