cvanderaa

We could have a vignette devoted to reading data with readQFeatures. It would provide a bit more details on how the function works and also provides concrete examples for the...

cf #206 for background This PR is still work in progress. One improvement could be to extend the section "*What about other input formats?*", where we could explicitely show different...

When `varFrom` and `varTo` are missing when calling `addAssayLink()`, the functions automatically matches the linked sets based on the rownames. This must be documented.

All QFeatures functions should add assays?

4

Our paradigm for QFeatures is that no data is removed or changed, it is only added. However, there are some functions that replace the assays. Here is a list: -...

During a discussion with Sam, we were wondering whether we could improve `sweep()`. The discussion only applies when `sweep`ing **multiple assays**. Consider the following example: ```r data("feat2") stats

Data sets may lack information about contaminant peptides when the user did not provide a contaminant database during raw data identification. We could provide functionality to automatically label peptide that...

Refactor: QFeatures subsetting

1

We could refactor subsetting and filtering of `Qfeatures` object. Here are some points I think would be worth improving for maintainability of the code: 1. In my opinion, filtering and...

There is a bug in `nNA()` when one assay is empty. ### Reproducible example ```r library(QFeatures) data("feat2") feat2[[1]]

feature request: filterNA() by column/sample

1

Currently, `filterNA()` remove rows/features in a particular assay that are missing above the provided threshold. I was wondering if it could also support filtering columns/samples, for instance by adding an...

feat: support an HDF5 backend for on-disk memory

1

This is a follow up on #157. For the moment, a `QFeatures` object is fully stored in memory. However, as assays in a `QFeatures` object are supposed to be processed...