Error while producing results
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
Start with the copykat v1.0.8 workflow shown in the report, focusing on step 9, “saving results,” where write.table reports that res is missing. Trace the preceding final-prediction step to determine why the reported run does not produce res, then confirm that the workflow completes and writes prediction.txt results.
Written by the indexing model from the issue text.
Description
Hi, could you please help me to understand what might be the issue:
[1] "running copykat v1.0.8 updated 02/25/2022 introduced mm10 module, fixed typos"
[1] "step1: read and filter data ..."
[1] "24879 genes, 101 cells in raw data"
[1] "18566 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= 369
number of iterations= 140
number of iterations= 229
number of iterations= 154
number of iterations= 165
number of iterations= 202
[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..."
Error in write.table(res, paste(sample.name, "prediction.txt", sep = ""), :
object 'res' not found
- Dominant language
- R
- Stars
- 305
- Forks
- 66
- PR merge metrics
- No merged PRs in 30d
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