added chromPeakSummary method #768
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jorainer
requested changes
Sep 20, 2024
R/XcmsExperiment.R
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| f <- factor(cp[,"sample"],seq_along(object)) | ||
| pal <- split.data.frame(cp[,c("mzmin","mzmax","rtmin","rtmax")],f) | ||
| names(pal) <- seq_along(pal) | ||
| ## Get integration function and other info. |
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you can drop these lines (2031:2034) as we don't need this.
R/XcmsExperiment.R
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| ":elapsed"), | ||
| total = length(chunks) + 1L, clear = FALSE) | ||
| pb$tick(0) | ||
| mzf <- "wMean" |
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also no need for this line as we don't need this variable.
R/XcmsExperiment.R
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| .xmse_integrate_chrom_peaks( | ||
| .subset_xcms_experiment(object, i = z, keepAdjustedRtime = TRUE, | ||
| ignoreHistory = TRUE), | ||
| pal = pal[z], intFun = .chrom_peak_beta_metrics, mzCenterFun = mzf, |
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i would change here to pal = pal[z], intFun = .chrom_peak_beta_metrics, BPPARAM = BPPARAM), we don't need the other parameters.
tests/testthat/test_XcmsExperiment.R
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| verboseBetaColumns = FALSE) | ||
| xmse <- findChromPeaks(mse, param = p) | ||
| res <- chromPeakSummary(res,BetaDistributionParam()) | ||
| expect_true(all(c("beta_cor", "beta_snr") %in% colnames(chromPeaks(res)))) |
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As detailed above, I would not replace the existing chromPeaks matrix with the metric, but have chromPeakSummary() returning the numeric matrix with the values of the metric.
jorainer
approved these changes
Sep 23, 2024
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As discussed with @jorainer I added the
chromPeakSummary()method which uses a new parameter class:BetaDistributionParam. It performs calculation of the new "beta quality metrics":beta_corandbeta_snron anXcmsExperimentobject for whichhasChromPeaks(object) = TRUE.I also added unit tests.
Johannes, feel free to let me know what I forgot and/or still need to add.
Thanks!