recalculateIntensity: Calculates area of peaks in peakTable

In Roestlab/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

For the give peak boundary in peakTable, the function extracts raw chromatograms and recalculate intensities.

Usage

recalculateIntensity(
  peakTable,
  dataPath = ".",
  oswMerged = TRUE,
  params = paramsDIAlignR()
)

Arguments

peakTable	(data-frame) usually an output of alignTargetedRuns. Must have these columns: run, precursor, 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 paramsDIAlignR function.

Value

(data-frame)

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-05-28

See Also

alignTargetedRuns, calculateIntensity

Examples

peakTable <- data.frame(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), stringsAsFactors = FALSE)
dataPath <- system.file("extdata", package = "DIAlignR")
newTable <- recalculateIntensity(peakTable, dataPath)

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.