const-ae / const-ae/tidygenomics
Wishlists and potential pull requests
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- R
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Description
I am really enjoying this package and I think a few functionalities may be added to this package. Wondering what your thoughts are?
- check data.frames: avoid a few common pitfalls in bioinformatics like `chr#` vs `#`, inconsistent headers etc.
Currently, the error message is a bit cryptic when chr numbering does not match:
```r
x1 <- data.frame(id = 1:4,
chromosome = c("chr1", "chr1", "chr2", "chr2"),
start = c(100, 200, 300, 400),
end = c(150, 250, 350, 450))
x2 <- data.frame(id = 1:4,
chromosome = c("1", "2", "2", "1"),
start = c(140, 210, 400, 300),
end = c(160, 240, 415, 320))
tidygenomics::genome_intersect(x1, x2, by=c("chromosome", "start", "end"), mode="both")
> tidygenomics::genome_intersect(x1, x2, by=c("chromosome", "start", "end"), mode="both")
Error: arrange() failed at implicit mutate() step.
✖ Could not create a temporary column for `..1`.
ℹ `..1` is `x`.
Run `rlang::last_error()` to see where the error occurred.
```
- strict conversion (in column headers) when converting between data.frame and GRanges
- other functionalities like `merge`
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