mixMetric: mixMetric

Description Usage Arguments Details Value References Examples

View source: R/otherMetrics.R

Description

mixMetric

Usage

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mixMetric(
  sce,
  group,
  k = 300,
  dim_red = "PCA",
  assay_name = "logcounts",
  n_dim = 10,
  k_pos = 5,
  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)).

k

Numeric. Number of k-nearest neighbours (knn) to use.

dim_red

Character. Name of embeddings to use as subspace for distance distributions. Default is "PCA".

assay_name

Character. Name of the assay to use for PCA. Only relevant if no existing 'dim_red' is provided.

n_dim

Numeric. Number of dimensions to include to define the subspace.

k_pos

Position of the cell, which rank to use for scoring, defaults to 5.

res_name

Character. Appendix of the result score's name (e.g. method used to combine batches).

Details

The mixMetric function implements the mixingMetric function from Seurat (See MixingMetric. It takes the median rank of the '__k_pos__ neighbour from each batch as estimation for the data's entropy according to the batch variable. The same result can be assesed using the MixingMetric function and a seurat object from the __Seurat__ package.

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

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library(SingleCellExperiment)
sim_list <- readRDS(system.file("extdata/sim50.rds", package = "CellMixS"))
sce <- sim_list[[1]][, c(1:15, 400:420, 16:30)]

sce <- mixMetric(sce, "batch", k = 20)

almutlue/CellMixS documentation built on Dec. 22, 2020, 11:07 a.m.