Error in match.arg(type) : 'arg' must be of length 1
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- r
- Domain
- data-visualization
Research direction
Reproduce the issue with the shown Seurat-derived count matrix and copykat call, then inspect the step 10 heatmap plotting path where match.arg(type) fails. Trace the type argument and identify why it is not length one; done means the run completes through heatmap generation without the error.
Written by the indexing model from the issue text.
Description
When I was running copyKAT from seurat object, the code is:
subset_count <- as.matrix(subset@assays$RNA@counts)
cnv <- copykat(rawmat=subset_count, ngene.chr=5, sam.name="copykat", n.cores=1)
Here is the running results:
[1] "running copykat v1.1.0"
[1] "step1: read and filter data ..."
[1] "17981 genes, 1800 cells in raw data"
[1] "7303 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
[1] "step 4: measuring baselines ..."
number of iterations= 665
number of iterations= 186
number of iterations= 3840
number of iterations= 139
number of iterations= 339
number of iterations= 210
[1] "step 5: segmentation..."
[1] "step 6: convert to genomic bins..."
[1] "step 7: adjust baseline ..."
[1] "step 8: final prediction ..."
[1] "step 9: saving results..."
[1] "step 10: ploting heatmap ..."
Error in match.arg(type) : 'arg' must be of length 1
what's the problem?
- Dominant language
- R
- Stars
- 305
- Forks
- 66
- PR merge metrics
- No merged PRs in 30d
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