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ADAT writer breaks with a single analyte soma_adat object #51

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stufield opened this issue May 30, 2023 · 0 comments · Fixed by #52
Closed

ADAT writer breaks with a single analyte soma_adat object #51

stufield opened this issue May 30, 2023 · 0 comments · Fixed by #52
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@stufield
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stufield commented May 30, 2023 •
edited

This is likely an corner case resulting from the apply() call expecting a 2nd dimension object but returning a vector ... see drop = FALSE to [.

out <- example_data[, seq(getMeta(example_data, n = TRUE) + 1L)]
write_adat(out, "foo.adat")

Timing solution:

n <- 1:100000
m <- matrix(n, nrow = 1)
bench::mark(
  mat = apply(m, 2, sprintf, fmt = "%0.1f"),
  vec = sprintf("%0.1f", n) 
)

Thanks for reporting 🥳!
@stufield stufield added the bug Something isn't working label May 30, 2023
stufield added a commit that referenced this issue May 30, 2023
@stufield
Bugfix for corner-case writing a single analyte ADAT
c0a3219 
- RFU values are rounded to 1 decimal during in `write_adat()`,
  via a call to `apply()`, which expects a 2-dim object when
  replacing those values.
- a single SOMAmer `soma_adat` will break unless `drop = FALSE`
- instead of this fix, convert the entire RFU
  data frame to a matrix (which maintains original dimensions)
  and use vectorized format conversion via `sprintf()`
- in theory this should be faster because `sprintf()`
  is only called once on a long vector, rather than
  1000s of times on shorter vectors.
- fixes #51
@stufield stufield mentioned this issue May 30, 2023
Merged
stufield added a commit that referenced this issue May 30, 2023
@stufield
Bugfix for corner-case writing a single analyte ADAT
a9ee8ce 
- RFU values are rounded to 1 decimal during in `write_adat()`,
  via a call to `apply()`, which expects a 2-dim object when
  replacing those values.
- a single SOMAmer `soma_adat` will break unless `drop = FALSE`
- instead of this fix, convert the entire RFU
  data frame to a matrix (which maintains original dimensions)
  and use vectorized format conversion via `sprintf()`
- in theory this should be faster because `sprintf()`
  is only called once on a long vector, rather than
  1000s of times on shorter vectors.
- fixes #51
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Bugfix write adat apply SomaLogic/SomaDataIO
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@stufield