Support chunk-wise processing in containsMz #341
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- Add support for chunk-wise processing to `containsMz()`. Related to issue #340.
| if (length(object)) { | ||
| cond_fun <- match.fun(match.arg(which)) | ||
| if (all(is.na(mz))) | ||
| return(rep(NA, length(object))) |
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I'm a bit confused, when do you use this function containsMz() exactly ? I saw the definition in the documentation but i've never had to use it before I think, so i'm not sure of the context where its usefull.
About this line of code above: Why would the variable mz be full of NA ?
Also the .has_mz_each() is not used here ? i'm a bit confused by the difference between .has_mz_each() and .peaks_contains_mz(), don't they both compare the mz() of a Spectra object to a numeric vector made of m/z values ?
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yes, in fact both do. I need to replace/remove also the .has_mz_each() function, but that will involve some bigger changes.
The .has_mz_each() and .has_mz() are old functions that simply run the code on all m/z values, without the possibility of chunk-wise processing or similar. This PR removes/replaces the .has_mz() function. I will then later also remove the other one. The difference between the two was: .has_mz() checks for presence of the same provided mz values in the m/z values of all spectra, while .has_mz_each() allowed to specify an individual (single!) mz value to check in a spectrum. Example: .has_mz(sps, mz = c(123.3, 234.12)) would check if any of the spectra have either an m/z value of 123.3 or 234.12. .has_mz_each(sps, mz = c(1, 2, 3, 4, 5)) checks if the first spectrum contains a 1, the second a 2 and so on - with the requirement length(sps) == length(mz).
Refactor
containsMz()to support chunk-wise processing.