Description Usage Arguments Details Note Author(s) See Also Examples
View source: R/functions-MSnExp.R
Estimate scattering of m/z values (due to technical, instrument specific noise) for the same ion in consecutive scans of a LCMS experiment.
estimateMzScattering(x, halfWindowSize = 1L, timeDomain = FALSE)
The m/z values of the same ions in consecutive scans (spectra) of a LCMS run will not be identical. This random noise is expected to be smaller than the resolution of the MS instrument. The distribution of differences of m/z values from neighboring spectra is thus expected to be (at least) bi-modal with the first peak representing the above described random variation and the second (or largest) peak the m/z resolution. The m/z value of the first local minimum between these first two peaks in the distribution is returned as the m/z scattering.
timeDomain = TRUE the function does not return the estimated
scattering of m/z values, but the scattering of
estimateMzResolution() for the function to estimate a
profile-mode spectrum's m/z resolution from it's data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
library(MSnbase) library(msdata) ## Load a profile-mode LC-MS data file f <- dir(system.file("sciex", package = "msdata"), full.names = TRUE) im <- readMSData(f, mode = "inMem", msLevel = 1L) res <- estimateMzScattering(im) ## Plot the distribution of estimated m/z scattering plot(density(unlist(res))) ## Compare the m/z resolution and m/z scattering of the spectrum with the ## most peaks idx <- which.max(unlist(spectrapply(im, peaksCount))) res[[idx]] abline(v = res[[idx]], lty = 2) estimateMzResolution(im[[idx]]) ## As expected, the m/z scattering is much lower than the m/z resolution.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.