recalculateIntensity {DIAlignR} | R Documentation |
For the give peak boundary in peakTable, the function extracts raw chromatograms and recalculate intensities.
recalculateIntensity( peakTable, dataPath = ".", oswMerged = TRUE, params = paramsDIAlignR() )
peakTable |
(data-table) usually an output of alignTargetedRuns. Must have these columns: precursor, run, intensity, leftWidth, rightWidth. |
dataPath |
(string) path to xics and osw directory. |
oswMerged |
(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet. |
params |
(list) parameters are entered as list. Output of the |
(data-table)
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-05-28
alignTargetedRuns, calculateIntensity
library(data.table) peakTable <- data.table(precursor = c(1967L, 1967L, 2474L, 2474L), run = rep(c("hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt", "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"), 2), intensity = c(186.166, 579.832, 47.9525, 3.7413), leftWidth = c(5001.76, 5025.66, 6441.51, 6516.6), rightWidth = c(5076.86, 5121.25, 6475.65, 6554.2)) dataPath <- system.file("extdata", package = "DIAlignR") params <- paramsDIAlignR() params$smoothPeakArea <- TRUE recalculateIntensity(peakTable, dataPath, params = params) peakTable <- data.table(precursor = c(1967L, 1967L, 2474L, 2474L), run = rep(c("hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt", "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"), 2), intensity = list(NA, NA, NA, NA), leftWidth = c(5001.76, 5025.66, 6441.51, 6516.6), rightWidth = c(5076.86, 5121.25, 6475.65, 6554.2)) params$transitionIntensity <- TRUE recalculateIntensity(peakTable, dataPath, params = params)