identifyNeighbors: identify shared nearest neighbors

In amsszlh/scMC: Integrating and comparing multiple single cell genomic datasets

Description

identify shared nearest neighbors

Usage

identifyNeighbors(
  object,
  mode = c("separate", "integrated"),
  nDims.pca = 40,
  force.pca = TRUE,
  nDims.knn = 40,
  k.param = 20,
  prune.SNN = 1/15,
  ...
)

Arguments

object	a lsit of Seurat objects or a single Seurat object
mode	"separate" or "integrate"
nDims.pca	the number of dimensions to use for running PCA
force.pca	Set force.pca = FALSE to skip the PCA calculation. Default = TRUE will calculate PCA.
nDims.knn	the number of dimensions to use for building SNN
k.param	Defines k for the k-nearest neighbor algorithm
prune.SNN	Sets the cutoff for acceptable Jaccard index when computing the neighborhood overlap for the SNN construction. Any edges with values less than or equal to this will be set to 0 and removed from the SNN graph. Essentially sets the strigency of pruning (0 — no pruning, 1 — prune everything).
...	other parameters in FindNeighbors

Value

seurat object

amsszlh/scMC documentation built on Jan. 2, 2021, 1:51 p.m.