locStructure: locStructure

In CellMixS: Evaluate Cellspecific Mixing

Description

locStructure

Usage

locStructure(
  sce,
  group,
  dim_combined,
  k = 100,
  dim_red = "PCA",
  assay_name = "logcounts",
  n_dim = 10,
  n_combined = 10,
  res_name = NULL
)

Arguments

sce	SingleCellExperiment object, with the integrated data.
group	Character. Name of group/batch variable. Needs to be one of names(colData(sce)).
dim_combined	Charactyer. Name of the reduced dimensional representation of the integrated data. Needs to be one of reducedDimNames(sce)).
k	Numeric. Number of k-nearest neighbours (knn) to use.
dim_red	Character. Name of embeddings to calculate neighbourhoods before integration. Default is "PCA".
assay_name	Character. Name of the assay to use for PCA of the original (not integrated) data. Should not refer to "corrected" counts.
n_dim	Numeric. Number of dimensions to include for the original data.
n_combined	Numeric. Number of dimensions to include for the integrated data.
res_name	Character. Appendix of the result score's name (e.g. method used to combine batches).

Details

The locStructure function implements the localStructure function from Seurat (See LocalStruct. For each group it calculates the k nearest neighbour within PCA space before integration and compares it to the knn within the reduced dimensional representation after integration. The score represents the proportion of overlapping neighbours. The LocalStruct function is based on the RunPCA function, while here runPCA is used. This can cause small deviance from the LocalStruct function, but overall these functions are equivalent.

Value

A SingleCellExperiment with the mixing metric within colData.

References

Stuart T Butler A Hoffman P Hafemeister C Papalexi E et. al. (2019) Comprehensive Integration of Single-Cell Data. Cell.

Examples

library(SingleCellExperiment)
sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
sce <- sim_list[["batch20"]][, c(1:50, 300:350)]

sce <- locStructure(sce, "batch", "MNN", k = 20, assay_name = "counts")

CellMixS documentation built on Dec. 19, 2020, 2 a.m.