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Add chromPeakSummary function and a fix #772
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- Report also a chromatogram's m/z values if `findChromPeaks` is run on a `Chromatogram` or `Chromatograms` object (issue #765).
- Peak shape quality (similarity to gaussian shape) calculation is now performed using the EIC representation of a chromatographic peak, i.e. with intensities of mass peaks for the same retention time (but different m/z) summed.
Add internal function to calculate beta metrics
added chromPeakSummary method
Added peak quality section to xcms vignette.
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This is great ! Also thanks for the small vignette ! The code looks good to me, thank @pablovgd, excited to incorporate it in the overall workflow and see how to integrate it with the other preprocessing steps to improve them.
PS: I think the GHA needs to be updated, i they are failing because of warnings.
R/XcmsExperiment-functions.R
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Looks great, thanks for implementing this! I haven't checked it for bugs but the logic looks sound.
Thanks @wkumler for your review! I have now addressed all your suggestions. |
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Hi, thanks for the PR !
What I couldn't attach to a specific line, would it make sense to add the paper to https://github.com/sneumann/xcms/blob/devel/inst/CITATION ?
Yours, Steffen
#' @param skews A numeric vector of the skews to try, corresponding to the | ||
#' shape1 of dbeta with a shape2 of 5. Values less than 5 will be increasingly | ||
#' right-skewed, while values greater than 5 will be left-skewed. | ||
#' shape1 of dbeta with a shape2 of 5. Values less than 5 will be |
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Hi @wkumler , I needed to read that a few times. So a value of 5 means symmetric ? Why is it not zero centered, so that abs()
tells you the skewedness (regardless in what direction) and you can <0
or >0
if you only want the direction ?
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That's a good point, thank you for the review. I'm using the language inherent to the dbeta()
function where the values of 2-5 correspond to the "positive parameters" alpha and beta (or, in R, shape1 and shape2). I'm absolutely open to rescaling these and I agree that a positive/negative skew would be more intuitive. If we're open to rescaling and we have a parameter to pass now in chromPeakSummary
then we also may want to allow a wider variety of numbers - the values of 5 matched my intuition for peak shape corners but other folks may want more/less tail and more/less skew.
@@ -279,6 +279,7 @@ dropGenericProcessHistory <- function(x, fun) { | |||
valsPerSpect = valsPerSpect, rtrange = rtr, | |||
mzrange = mzr) | |||
if (length(mtx)) { | |||
## mtx: time, mz, intensity | |||
if (any(!is.na(mtx[, 3]))) { |
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I usually recommend avoiding hardcoded column numbers, imagine someone came up with (time, ccs, mz, intensity)
. Might need that mtx is created with named columns somewhere above. Is that the only occurance of a hardcoded column number in the PR ?
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I agree - generally. Here, we load the mtx
matrix
with a function that is supposed to return a 3 column matrix with the columns exactly in the expected order. Thus, IMHO for this case (as long as there is no user input involved) it's save to use access-by-index. Also, because here we're calling this in a loop thousands of times, the way how we subset could affect the performance.
I did some timings on that:
mtx <- cbind(time = 1:5, mz = 1:5, intensity = c(2342.2, 123.1, 231.1, 23.1, 123.23))
int_col <- 3L
library(microbenchmark)
> microbenchmark(mtx[, 3L], mtx[, "intensity"], mtx[, int_col])
Unit: nanoseconds
expr min lq mean median uq max neval cld
mtx[, 3L] 354 363.5 437.30 380.5 477.5 948 100 a
mtx[, "intensity"] 389 404.0 543.07 412.0 474.0 5036 100 a
mtx[, int_col] 381 399.5 469.45 407.0 484.0 1135 100 a
((rtr[2] - rtr[1]) / | ||
max(1, (sum(rtim >= rtr[1] & rtim <= rtr[2]) - 1))) | ||
maxi <- which.max(mtx[, 3]) | ||
maxi <- which.max(mtx[, 3L]) |
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No, above was not the only hardcoded 3
:-) and more below ...
Regarding the CITATIONS - I added the reference to the respective man page. I think adding that as a CITATION for xcms itself might be bit too much, as the paper deals more with peak shape quality, independently of xcms? |
For now I only bumped the version and fixed the NEWS.md, but I did not address the other points above - can we maybe discuss them again @sneumann ? |
I'll make the PR a draft and fix the conflicts. After that I'll re-open. |
- Add `c()` method to combine `XcmsExperiment` objects. - Add a method to coerce from `XCMSnExp` to `XcmsExperiment` objects. - Fix references in documentation.
I've now fixed the conflicts and in addition also added the |
This PR adds the
chromPeakSummary()
method and a first implementation to calculate the peak shape quality from @wkumler on chrom peak results (thanks to @pablovgd for contributing).In addition, it fixes a bug in the calculation of the beta scores during gap filling.