validateMatchedSpectra: Validating MatchedSpectra

In rformassspectrometry/MetaboAnnotation: Utilities for Annotation of Metabolomics Data

Validating MatchedSpectra

Description

The validateMatchedSpectra() function opens a simple shiny application that allows to browse results stored in a MatchedSpectra object and to validate the presented matches. For each query spectrum a table with matched target spectra are shown (if available) and an interactive mirror plot is generated. Valid matches can be selected using a check box which is displayed below the mirror plot. Upon pushing the "Save & Close" button the app is closed and a filtered MatchedSpectra is returned, containing only validated matches.

Note that column "query_index_" and "target_index_" are temporarily added to the query and target Spectra object to display them in the interactive graphics for easier identification of the compared spectra.

Usage

validateMatchedSpectra(object)

Arguments

object

A non-empty instance of class MatchedSpectra.

Value

A MatchedSpectra with validated results.

Author(s)

Carolin Huber, Michael Witting, Johannes Rainer

Examples

library(Spectra)
## Load test data
fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
pest_ms2 <- filterMsLevel(Spectra(fl), 2L)
pest_ms2 <- pest_ms2[c(808, 809, 945:955)]
load(system.file("extdata", "minimb.RData", package = "MetaboAnnotation"))

## Normalize intensities and match spectra
csp <- CompareSpectraParam(requirePrecursor = TRUE,
                           THRESHFUN = function(x) x >= 0.7)
norm_int <- function(x) {
    x[, "intensity"] <- x[, "intensity"] / max(x[, "intensity"]) * 100
    x
}
ms <- matchSpectra(addProcessing(pest_ms2, norm_int),
                   addProcessing(minimb, norm_int), csp)

## validate matches using the shiny app. Note: the call is only executed
## in interactive mode.
if (interactive()) {
    res <- validateMatchedSpectra(ms)
}

rformassspectrometry/MetaboAnnotation documentation built on Dec. 20, 2024, 6:55 a.m.