Why getting error in executing open_loom command in SCENIC

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

software error rna-seq rna-seq

• 3,426 views • link

updated 5.9 years ago by kentasticks •

• written 6.1 years ago by inayat45shaikh •

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

Thanks Inayat

• 0 views • link

written 5.9 years ago by inayat45shaikh •

2 answers

It might be due to a bug in the SCopeLoomR.

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

Vincent

• 0 views • link

written 5.9 years ago by abysslover •

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

• 0 views • link

written 5.9 years ago by kentasticks •