Update RNAIntegration.R #2178
Open
Update RNAIntegration.R #2178
Conversation
This file contains 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
Update auto-comment.yml
Update auto-comment.yml
when running addGeneIntegrationMatrix function, it will occur this error: "Error in slot(object = object, name = \"features\")[[layer]] <- features : \n more elements supplied than there are to replace\n" After repeated testing, I finally know the answer to this question： This error occurred in the RNAIntegration.R of the ArchR package This code in the RNAIntegration.R file: seuratATAC <- Seurat::CreateSeuratObject(counts = mat[head(seq_len(nrow(mat)), 5), , drop = FALSE]) The Seurat::CreateSeuratObject function requires that the rownames of mat must be vector, not matrix. But the rownames passed to mat in the previous code was actually a matrix, so you only need to add a command line before this code, this will cast the rownames of mat to a vector: rownames(mat) <- as.character(rownames(mat)) And then this error was completely eliminated.
halaszlaszlo
approved these changes
Nov 1, 2024
|
Hi ZhangFuchang, thanks for this! I've been noticing this was breaking tests starting at R 4.2/4.3 or so. I'll merge in, but do you mind setting your local upstream as the dev branch? I would like to provide you credit for this, but I do not want the changes from |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
when running addGeneIntegrationMatrix function, it will occur this error: "Error in slot(object = object, name = "features")[[layer]] <- features : \n more elements supplied than there are to replace\n"
After repeated testing, I finally know the answer to this question： This error occurred in the RNAIntegration.R of the ArchR package This code in the RNAIntegration.R file: seuratATAC <- Seurat::CreateSeuratObject(counts = mat[head(seq_len(nrow(mat)), 5), , drop = FALSE]) The Seurat::CreateSeuratObject function requires that the rownames of mat must be vector, not matrix. But the rownames passed to mat in the previous code was actually a matrix, so you only need to add a command line before this code, this will cast the rownames of mat to a vector: rownames(mat) <- as.character(rownames(mat))
And then this error was completely eliminated.