check_spe: Check input spe

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

Check input spe

Description

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

Usage

check_spe(
  spe,
  variables = c("sum_umi", "sum_gene", "expr_chrM", "expr_chrM_ratio")
)

Arguments

spe	Defaults to the output of fetch_data(type = 'spe'). This is a SpatialExperiment-class object with the spot-level Visium data and information required for visualizing the histology. See fetch_data() for more details.
variables	A character() vector of variable names expected to be present in colData(spe).

Value

The input object if all checks are passed.

Author(s)

Brenda Pardo, Leonardo Collado-Torres

See Also

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

Examples

if (enough_ram()) {
    ## Obtain the necessary data
    if (!exists("spe")) spe <- fetch_data("spe")

    ## Check the object
    check_spe(spe)
}

LieberInstitute/spatialLIBD documentation built on April 21, 2024, 6:47 p.m.