Error : object 'anno.mat' not found
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
The entry point is the shown copykat(...) call; begin by reproducing the step 2 annotation gene coordinates stage with the Seurat counts and hg38 settings. Check how the input row names are matched to the annotation data, and consider the reported removal of ENSG identifiers; done when the run proceeds past the missing anno.mat error.
Written by the indexing model from the issue text.
Description
Hi copyKAT team,
I wanted to run copyKAT on a single-cell data but I encountered an error:
> copykat.test <- copykat(rawmat=copyKAT.input,
+ id.type="S",
+ ngene.chr=5,
+ win.size=25,
+ KS.cut=0.1,
+ sam.name="test",
+ distance="euclidean",
+ norm.cell.names="",
+ output.seg="FLASE",
+ plot.genes="TRUE",
+ genome="hg38",
+ n.cores=4)
[1] "running copykat v1.1.0"
[1] "step1: read and filter data ..."
[1] "25644 genes, 39717 cells in raw data"
[1] "8849 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
Error in copykat(rawmat = copyKAT.input, id.type = "S", ngene.chr = 5, :
object 'anno.mat' not found
I prepared my input matrix from my Seurat object by extracting the raw counts table.
copyKAT.input <- seuratobject@assays$RNA$counts
cellranger uses both Gene symbols and Ensembl identifiers for the genes, so I removed those genes that have Ensembl IDs:
copyKAT.input <- copyKAT.input[!grepl("^ENSG", rownames(copyKAT.input)), ]
However, I still got the same error.
The single cell data is from human and was made by cellranger-9.0.1 and GRCh38-2024-A.
Could you please suggest a solution for this error?
Many thanks for your help in advance.
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- R
- Stars
- 305
- Forks
- 66
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