read10xVisiumAnalysis: Load analysis data from a 10x Genomics Visium experiment

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

Load analysis data from a 10x Genomics Visium experiment

Description

This function expands SpatialExperiment::read10xVisium() by reading analysis outputs from SpaceRanger by 10x Genomics.

Usage

read10xVisiumAnalysis(
  samples = "",
  sample_id = paste0("sample", sprintf("%02d", seq_along(samples)))
)

Arguments

samples	Passed to SpatialExperiment::read10xVisium().
sample_id	Passed to SpatialExperiment::read10xVisium().

Details

You might want to use read10xVisiumWrapper() instead of using this function directly.

Value

A named list() with the information about the clustering and the dimension reduction (projections) from the SpaceRanger output by 10x Genomics.

See Also

Other Utility functions for reading data from SpaceRanger output by 10x Genomics: add10xVisiumAnalysis(), read10xVisiumWrapper()

Examples

## See 'Using spatialLIBD with 10x Genomics public datasets' for
## a full example using this function.
if (interactive()) {
    browseVignettes(package = "spatialLIBD")
}

## Note that ?SpatialExperiment::read10xVisium doesn't include all the files
## we need to illustrate read10xVisiumWrapper().

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