Skip to content

Make facilitate more robust to crazy fdata() data.frames #4

@lianos

Description

@lianos

I had a DGEList with some crazy y$genes data.frame. Had columns named NA and other stuff. It totally screwed things in weird places.

For instance a call to fdge in something like:

y.all %>%
  facilitate() %>%
  flm_def("group", "a", "b") %>%
  fdge()

would throw a crazy error like this:

Error in initialize(...) : attempt to use zero-length variable name
exiting from: biocbox.FacileLinearModelDefinition(x, assay_name, method, features, 
    filter, with_sample_weights = with_sample_weights, weights = weights, 
    ...)
Error in fdge.FacileLinearModelDefinition(., method = "voom") : 
  rownames of design(x) does not match biocbox

and it turned out that crappy column names in the features() we were getting was the problem

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions