bam.test.obj <- CellTagMatrixCount(celltag.obj = bam.test.obj, barcodes.file = "./barcodes_all.tsv")
Closed this issue · 5 comments
bam.test.obj <- CellTagMatrixCount(celltag.obj = bam.test.obj, barcodes.file = "./barcodes_all.tsv")
Warning message:
In [.data.table(alltagCounts, , :=((tagsRemove), NULL)) :
length(LHS)==0; no columns to delete or assign RHS to.
The above error was reported in this step，I think the number of rows may be exceed the boundary, so how can I deleted some number of rows to adapt to the conditions ? thanks
Hello,
Thank you for using CellTagR!
In this step, we are trying to remove CellTags that have zero UMI count across all cells. I think this warning suggests that all CellTags have at least 1 UMI count and nothing is removed . And it should not affect the result matrix construction and downstream analysis.
Hope this helps! Please let us know if there is any other issues!
Best,
Wenjun
Can you give me the code of removing CellTags，I'm not proficient in R，thanks again
I have deleted all cells in which UMI was expressed only once, and the number of rows of bam.parse.rslt[["v1"]] was reduced to 4,543,130, but the same error was still reported
As you have mentioned above, I just want to double check - is the following the error reported?
Warning message:
In [.data.table(alltagCounts, , :=((tagsRemove), NULL)) :
length(LHS)==0; no columns to delete or assign RHS to.
If so, it can be ignored because it is a warning message and it should have successfully produced the matrix in the @raw.count. Please let us know if there are any additional error messages!
Sorry for the confusion and hope this helps!
Best,
Wenjun
It works fine, but it appears to have not generated correlation matrix in this step, "bam.test.obj <- JaccardAnalysis(bam.test.obj)", I can generate correlation matrix when I run a single BAM file, but now running two BAM files will not generate it.