MixingMetric: Calculates a mixing metric

In Seurat: Tools for Single Cell Genomics

Calculates a mixing metric

Description

Here we compute a measure of how well mixed a composite dataset is. To compute, we first examine the local neighborhood for each cell (looking at max.k neighbors) and determine for each group (could be the dataset after integration) the k nearest neighbor and what rank that neighbor was in the overall neighborhood. We then take the median across all groups as the mixing metric per cell.

Usage

MixingMetric(
  object,
  grouping.var,
  reduction = "pca",
  dims = 1:2,
  k = 5,
  max.k = 300,
  eps = 0,
  verbose = TRUE
)

Arguments

object	Seurat object
grouping.var	Grouping variable for dataset
reduction	Which dimensionally reduced space to use
dims	Dimensions to use
k	Neighbor number to examine per group
max.k	Maximum size of local neighborhood to compute
eps	Error bound on the neighbor finding algorithm (from RANN)
verbose	Displays progress bar

Value

Returns a vector of values of the mixing metric for each cell

Seurat documentation built on Nov. 18, 2023, 1:10 a.m.