Switching from summarise() to reframe() to avoid dplyr warnings #518
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cying111
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Jan 9, 2026
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tested on test data, looks all good to me.
lingminhao
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Jan 9, 2026
| hitsDF <- hitsDF %>% dplyr::select(queryHits, chr, start, end, strand) %>% | ||
| group_by(queryHits, chr, strand) %>% | ||
| summarise(start = max(start), end = min(end), .groups = "drop") %>% | ||
| reframe(.by = c(queryHits, chr, strand), start = max(start), end = min(end)) %>% ungroup() %>% |
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no need ungroup() after reframe()
lingminhao
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reframe() gives ungrouped data frame, so ungroup() is redundant (for example above). Other than that, the change looks good to me.
It resolved the github issue #502
cying111
reviewed
Jan 12, 2026
| txScore.noFit = weighted.mean(txScore.noFit, readCount_tmp)) %>% | ||
| group_by(chr, strand, start, end) %>% | ||
| summarise(readCount = sum(readCount), | ||
| reframe(.by = c(chr, strand, start, end), |
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I think the warning really is coming from this usage only, where txScore is from multiple samples, hence, multiple rows will be produced in this step.
A quick fix would be change it to mutate, cause there is no summarising happening at this step.
All the other instances of summarise no need to change actually. I have tested on my side for this.
Thanks
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