Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

subset not working as expected #258

Open
jvolkening opened this issue Oct 13, 2021 · 0 comments
Open

subset not working as expected #258

jvolkening opened this issue Oct 13, 2021 · 0 comments

Comments

@jvolkening
Copy link

Hello,

I've been using kallisto/sleuth for DE analysis of a virus/host dataset. It has been working well for analysing the full transcript set, but now I would like to normalize and analyze only the viral genes separately. I have tried to use the following code to subset the kallisto objects:

# old_path and new_path point to locations of existing and to-be-created HDF5 files
dir.create(dirname(new_path), recursive=T)
read_kallisto_h5(old_path, read_bootstrap=T) %>%
    subset_kallisto(target_ids=viral_ids) %>%
    write_kallisto_hdf5(fname=new_path)

This runs without error, but after troubleshooting subsequent sleuth errors and dumping the contents of the newly written HDF5 files, I found that all of the datasets in the new HDF5 are empty except for bias_observed, bias_normalized, fld, and the bootstrap datasets. For instance, the ids dataset is empty, which was the initial source of my downstream problems. I did double-check that viral_ids were correct and matched those used in kallisto, and sleuth reports the expected number of transcripts filtered.

It appears the problem is in subset_kallisto(), since if I don't subset and only read/write directly, the created HDF5 file seems to be valid. I have seen similar issues, e.g. #204, but I'm not sure if they are directly related or not.

I just tried with sleuth installed from GitHub today using devtools, with the same result.

Thanks in advance for any help.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant