Closed m-zaki closed 5 years ago
Hi Zaki
You have a valid point, although this is not yet supported. For our benchmark the main idea was that the developer of a method decides what normalisation is most appropriate for their method. From a user perspective, this is perhaps not always the most desirable behaviour... At the moment, we're redesigning the way each method is wrapped, so I can't easily add this behaviour now, but will have another look in a couple of weeks once these updates are integrated!
Thanks for trying out the package Wouter
Dear authors,
Thanks for the great package.
I was wondering if there is a way to select for the expression values while using
infer_trajectory
Please find an example below;Creating the dataset (sce referes to SingleCellExperiment object)
After selecting the guidelines with the shinyapp, proceed to infer trajectory
model <- infer_trajectory(dataset, "slingshot", verbose=TRUE")
Which returns the following.
Executing 'slingshot' on '20190226_084323__data_wrapper__SETXwUVAWV' With parameters: list(shrink = 1, reweight = TRUE, reassign = TRUE, thresh = 0.001, maxit = 10L, stretch = 2, smoother = "smooth.spline", shrink.method = "cosine") And inputs: counts, start_id
I was wondering, how could we selct for a different expression input for slingshot? Specifcally if I want to use the normalised expression that has been log-transformed. Therefore I would like to skip the default log transformation.
Many thanks again for the great package
Best Zaki