stabMapSE: Stabilised mosaic single cell data integration using unshared...

In MarioniLab/StabMap: Stabilised mosaic single cell data integration using unshared features

Stabilised mosaic single cell data integration using unshared features

Description

stabMapSE performs StabMap with SummarizedExperiment type (SingleCellExperiment, SpatialExperiment) objects as input.

Usage

stabMapSE(..., assays = "logcounts", args = list())

Arguments

...	Set of SummarizedExperiment, SingleCellExperiment, SpatialExperiment, etc that should be named.
assays	Named character vector of assays to be extracted from the objects.
args	List of arguments to be passed on to 'stabMap'

Value

matrix containing common embedding with rows corresponding to cells, and columns corresponding to PCs or LDs for reference dataset(s).

Examples

set.seed(2021)
library(SingleCellExperiment)

sce_1 = SingleCellExperiment(assays = list(logcounts = mockMosaicData(names = "D1", ncells = 1000, ngenes = list(1:500))[[1]]))
sce_2 = SingleCellExperiment(assays = list(logcounts = mockMosaicData(names = "D2", ncells = 1000, ngenes = list(251:750))[[1]]))
sce_3 = SingleCellExperiment(assays = list(counts = mockMosaicData(names = "D3", ncells = 1000, ngenes = list(500:750))[[1]]))

out = stabMapSE(D1 = sce_1, D2 = sce_2)

# pass on additional parameters to stabMap()
# e.g. change number of components of reference
out = stabMapSE(D1 = sce_1, D2 = sce_2, args = list(ncomponentsReference = 20))
dim(out)

# pull out different assay names:
out = stabMapSE(D2 = sce_2, D3 = sce_3, assays = c("D2" = "logcounts", "D3" = "counts"))

MarioniLab/StabMap documentation built on Sept. 28, 2022, 2:28 a.m.