Code for reading h5ad files in R

Question

[JACKY]

How can I read and view h5ad files in R? I tried the Seurat package but I see no function that can read such files. I found another package called SeuratDisk but it's confusing.

Say I have a file called GSE123456.h5ad, how do I read it?

Answer 1

[fracarb8]

What do you find confusing about SeuratDisk? The documentation literately gives you the code:

# docu example
Convert("pbmc3k_final.h5ad", dest = "h5seurat", overwrite = TRUE)
pbmc3k <- LoadH5Seurat("pbmc3k_final.h5seurat")

[JACKY]

The reason I said its confusing is because I got errors. So for the code you provided here is the result :

> GSE120575 = SeuratDisk::LoadH5Seurat("singleCell/GSE120575.h5seurat")

Validating h5Seurat file
Initializing RNA with data
Error in sparseMatrix(i = x[["indices"]][] + 1, p = x[["indptr"]][], x = x[["data"]][],  : 
  'dims' must contain all (i,j) pairs

Any idea what this error is ? thank you!

[Ram]

Where did you get the initial h5ad file from? Are you sure it is not corrupt?

[JACKY]

It's not corrupt because when I tried reading it with python it worked:

import anndata
adata = anndata.read_h5ad("GSE123456.h5ad")

And I can access, for example, the number of genes and the number of observations :

num_observations = adata.obs.shape[0]
print(f"Number of observations: {num_observations}")

num_genes = adata.var.shape[0]
print(f"Number of genes: {num_genes}")

Number of observations: 60
Number of genes: 14654

[fracarb8]

are you using seurat v5? Do you get the error if you set options(Seurat.object.assay.version = "v3")?