A little suggestion of update to make ROGUE suitable for large dgCMatrix data#8
Open
mimi3421 wants to merge 2 commits intoPaulingLiu:masterfrom
Open
A little suggestion of update to make ROGUE suitable for large dgCMatrix data#8mimi3421 wants to merge 2 commits intoPaulingLiu:masterfrom
mimi3421 wants to merge 2 commits intoPaulingLiu:masterfrom
Conversation
Make ROGUE suitable for large dgCMatrix data
Update the old ROGUE to new
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Dear author,
I have used ROGUE in place of the default HVG algorithm for feature sellection in the fastMNN pipeline and found that it returned a more concise UMAP graph and a more reasonable result in functional analysis after clustering.
I make a little change to reduced the RAM footprint and summit here if someone need it.
As
log(0+1)=0, I make a little change in theEntropyfunction so that only the non-zero log result will be updated whendgCMatrixis supplied as the input data matrix, which would greatly reduce the RAM consumption.