Why getting error in executing open_loom command in SCENIC

Question

[inayat45shaikh]

Hello, I am trying executing example datasets in SCENIC R workflow, but getting error in loading loom file.

Here is the command i am using

loomPath <- system.file(package="SCENIC", "examples/mouseBrain_toy.loom") library(SCopeLoomR) loom <- open_loom(loomPath, mode="r")

Error in x$create_attr(which, robj = value) : HDF5-API Errors: error #000: ../../../src/H5A.c in H5Acreate2(): line 267: no write intent on file class: HDF5 major: Invalid arguments to routine minor: Write failed

could anyone help me fixing this issue.

Thanks Inayat

[inayat45shaikh]

Thanks for the suggestion, I will try this.....

Thanks Inayat

Answer 1

[abysslover]

It might be due to a bug in the SCopeLoomR.

Try to replace open_loom() with H5File$new() and see if it works.

Vincent

Answer 2

[kentasticks]

Hello Using loomR::connect() function insted of open_loom() was good alternative in my case. "connect(path, mode = "r+")" will work. After loading data, you can access the contents by SCopeLoomR functions(). Thank you.

Takahashi