Download the ulcerative colitis example data for DIALOGUE

This function downloads the ulcerative colitis subset used by the DIALOGUE paper into the temporary directory. 5,374 cells across five cell subtypes and 30 donors, with the inflammation status per biopsy. Enough samples per cell type for dialogue_sc(), which most single sample example data sets are not.

Usage

download_dialogue_uc(quiet = FALSE)

Arguments

quiet

Boolean. If the download shall be quiet.

Value

String. The path to the ulcerative colitis h5ad file.

Details

The published matrix holds log2(TPM / 10 + 1), which is what Smillie, et al. released; the raw counts were never published. The file served here has been linearised back to the TPM/10 scale and rounded, so it loads through load_h5ad() like any count matrix and gets bixverse's own log CPM on the way in. See data-raw/dialogue_uc.R for the preparation.

References

Smillie, et al., Cell, 2019; Jerby-Arnon and Regev, Nat. Biotechnol., 2022

Examples

if (FALSE) { # \dontrun{
# pulls the archive into the session tempdir()
path <- download_dialogue_uc()
get_h5ad_dimensions(path)$dims
} # }