cvanderaa
cvanderaa
This issue is to keep track of the progress of the unit testing. Unit test should be written for the function in the following scripts: - [x] `R/ScpModel-Class.R` - [x]...
We should explicitly document in the vignette how to make additional useful visualisation. Current ideas: ## Intensity plot Show peptide/protein intensities vs other covariates. Eg (from [scplainer article](https://github.com/UCLouvain-CBIO/2023-scplainer/blob/13726cd3e76de008be92b996e65991e1ef2d3111/3_make_figures/make_figure2.R#L101C1-L116C25)):  Code...
The issues has been highlighted in: https://github.com/UCLouvain-CBIO/scp/issues/56#issuecomment-2010539916 The reason is that the subsetting functionality in `QFeatures` does not know it should also subset the `ScpModel` objects contained in `metadata(qfObject)`. A...
As requested by the Slavov lab. A concern for new users is 'will my data work with scp'? Lower that barrier is essential! GUIs can be a good way to...
Let's have a function that computes a metric or statistic for every cell across several batches. The function would be a generalization of `computeMedianCVperCell()`. *Tentative signature*: `computePerCell(object, i, colDataName, FUN,...
(The current issue is more of a food for thought than an actual issue. Still, I think our package could clarify the concept of coefficient of variation (CV) a bit...
I think we should consider several improvements: 1. `divideByReference()` is a type of normalization (normalization by reference channel), therefore I think it should be made accessible from `normalizeSCP()`. This means...
I need to aggregate PSMs -> peptides and peptides -> proteins @lgatto from reading the documentation I understand I need to log transform the **PSM intensities** before aggregation with `robustSummary`...
Currently there are 2 ways to extract a set. Suppose `qf` is a `QFeatures` object with 1 or more sets: ```r qf[["setOfInterest"]] ## 1. getWithColData(qf, "setOfInterest") ## 2. ``` Option...
Curently, `joinAssays()` combines multiple sets into a new set by matching rownames. However, in some cases, the rownames may not be meaningful for joining and I would prefer to join...