recalculateIntensity {DIAlignR} | R Documentation

## Calculates area of peaks in peakTable

### 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-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 `paramsDIAlignR` function.

### Value

(data-table)

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

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

### See Also

`alignTargetedRuns, calculateIntensity`

### Examples

    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)

[Package DIAlignR version 2.2.0 Index]