check_sce_layer: Check input sce_layer

In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Check input sce_layer

Description

This function checks that the sce_layer object has the appropriate structure. For more details please check the vignette documentation.

Usage

check_sce_layer(sce_layer, variables = "spatialLIBD")

Arguments

sce_layer	Defaults to the output of fetch_data(type = 'sce_layer'). This is a SingleCellExperiment object with the spot-level Visium data compressed via pseudo-bulking to the layer-level (group-level) resolution. See fetch_data() for more details.
variables	A character() vector of variable names expected to be present in colData(sce_layer).

Value

The input object if all checks are passed.

See Also

Other Check input functions: check_modeling_results(), check_sce(), check_spe()

Examples

## Obtain example data from the HumanPilot project
## (Maynard, Collado-Torres, et al, 2021)
if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")

## Check the pseudo-bulked data
check_sce_layer(sce_layer)

LieberInstitute/spatialLIBD documentation built on Dec. 19, 2024, 7:12 p.m.