data: Synthetic single-cell, mixture and marker data

In MarcElosua/SPOTlight: `SPOTlight`: Spatial Transcriptomics Deconvolution

Synthetic single-cell, mixture and marker data

Description

mockSC/mockSP() are designed to generate synthetic single-cell and spatial mixture data. These data are not meant to represent biologically meaningful use-cases, but are solely intended for use in examples, for unit-testing, and to demonstrate SPOTlight's general functionality. Finally, .get_mgs() implements a statistically naive way to select markers from single-cell data; again, please don't use it in real life.

Usage

mockSC(ng = 200, nc = 50, nt = 3)

mockSP(x, ns = 100)

getMGS(x, n_top = 10)

Arguments

ng, nc, nt, ns	integer scalar specifying the number of genes, cells, types (groups) and spots to simulate.
x	Single cell experiment object
n_top	integer specifying the number of marker genes to extract for each cluster.

Value

• mockSC returns a SingleCellExperiment with rows = genes, columns = single cells, and cell metadata (colData) column type containing group identifiers.

• mockSP returns a SingleCellExperiment with rows = genes, columns = single cells, and cell metadata (colData) column type containing group identifiers.

• getMGS returns a data.frame with nt*n_top rows and 3 columns: gene and type (group) identifier, as well as the gene's weight = the proportion of counts accounted for by that type.

Examples

sce <- mockSC()
spe <- mockSP(sce)
mgs <- getMGS(sce)

MarcElosua/SPOTlight documentation built on March 7, 2024, 4:58 p.m.