medianPrecursorMz | R Documentation |
"Median m/z value for all identified peptides (unique ions) after FDR." [PSI:QC] id: QC:4000065
The metric is calculated as follows: (1) the 'Spectra' object is filtered according to the MS level,
(2) the precursor m/z values are obtained,
(3) the median value is returned ('NAs' are removed).
medianPrecursorMz(spectra, msLevel = 1L, ...)
spectra |
'Spectra' object |
msLevel |
'integer' |
... |
not used here |
is_a: QC:4000003 ! single value is_a: QC:4000009 ! ID based is_a: QC:4000023 ! MS1 metric is_a: QC:4000025 ! ion source metric
'numeric(1)'
'medianPrecursorMz' will calculate the *precursor* median m/z of all Spectra within 'spectra'. If the calculation needs be done according to *QC:4000065*, the 'Spectra' object should be prepared accordingly, i.e. filtered with e.g. [filterPrecursorMz()] or subsetted to spectra with identification data.
Thomas Naake, thomasnaake@googlemail.com
library(S4Vectors) library(Spectra) spd <- DataFrame( msLevel = c(2L, 2L, 2L), polarity = c(1L, 1L, 1L), id = c("HMDB0000001", "HMDB0000001", "HMDB0001847"), name = c("1-Methylhistidine", "1-Methylhistidine", "Caffeine")) ## Assign m/z and intensity values spd$mz <- list( c(109.2, 124.2, 124.5, 170.16, 170.52), c(83.1, 96.12, 97.14, 109.14, 124.08, 125.1, 170.16), c(56.0494, 69.0447, 83.0603, 109.0395, 110.0712, 111.0551, 123.0429, 138.0662, 195.0876)) spd$intensity <- list( c(3.407, 47.494, 3.094, 100.0, 13.240), c(6.685, 4.381, 3.022, 16.708, 100.0, 4.565, 40.643), c(0.459, 2.585, 2.446, 0.508, 8.968, 0.524, 0.974, 100.0, 40.994)) spd$precursorMz <- c(170.16, 170.16, 195.0876) sps <- Spectra(spd) medianPrecursorMz(spectra = sps, msLevel = 2L)
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