registration_block_cor: Spatial registration: block correlation

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

Spatial registration: block correlation

Description

This function computes the block correlation using the sample ID as the blocking factor. This takes into account that cells in scRNA-seq data or spots in spatially-resolved transcriptomics data from Visium (or similar) have a sample ID batch effect.

Usage

registration_block_cor(
  sce_pseudo,
  registration_model,
  var_sample_id = "registration_sample_id"
)

Arguments

sce_pseudo	The output of registration_pseudobulk().
registration_model	The output from registration_model().
var_sample_id	A character(1) specifying the colData(sce_pseudo) variable with the sample ID.

Value

A numeric(1) with the block correlation at the sample ID level.

See Also

Other spatial registration and statistical modeling functions: registration_model(), registration_pseudobulk(), registration_stats_anova(), registration_stats_enrichment(), registration_stats_pairwise(), registration_wrapper()

Examples

example("registration_model", package = "spatialLIBD")
block_cor <- registration_block_cor(sce_pseudo, registration_mod)

LieberInstitute/spatialLIBD documentation built on Nov. 4, 2024, 11:57 a.m.