Browse visually an Annot object

Source: R/app.R

MS2IDgui is a Shiny app that visually browses the annotation results stored in an Annot object. The Annot object can be loaded as an argument or directly from the user interface.

MS2IDgui(annot)

Arguments

annot

Annot object with the results to be browsed. By default (no argument), the function opens the browser with no data and the Annot object can be loaded using the user interface.

Details

The user interface has two panels. The right panel lists the loaded annotations as rows in a table; when one of them is clicked, the left panel responds by displaying the figures related to the selection:

  • Tab Cons.: If the annotation has a consensual query spectrum, this sub-panel displays a figure with the query spectra that form it..

The left panel also has two more tabs with general features:

  • Tab Info: Lists the arguments used in the annotate function that resulted in the present Annot object.

Concerning the right panel, it must be noted: The

  • Every row corresponds to an annotation in the table, and different annotations of the same spectrum have identical row colours.

  • Column names that contain QRY, REF or CONS refer to query, reference or consensus entities, respectively. e.g. QRYprecursorMz contains the precursor M/z of the query spectra, REFadduct the adducts of the reference spectra and QRYrtime_CONS the retention times of the query spectra that conform every consensus spectrum.

  • The column massNum refers to the number of fragments of the query spectrum (green), the reference spectrum (red) and the number of fragments in common (black). Similarly, the column collisionEnergy shows the collision energy of the query (green) and reference (red) spectra.

  • REFinchikey shows the inchikey of the reference compound and links to a Pubchem's page with a list of compounds that shares that inchikey.

  • ppmPrecMass refers to the absolute difference value in ppm between query and reference precursor masses.

See also

Annot class and annotate function.

Author

Josep M. Badia josepmaria.badia@urv.cat

Examples


## LOAD MS2ID LIBRARY ---
## Decompress the MS2ID library that comes with MS2ID
MS2IDzipFile <- system.file("extdata/MS2IDLibrary.zip",
                            package = "MS2ID",
                            mustWork = TRUE)
library(utils)
MS2IDFolder <- dirname(unzip(MS2IDzipFile,
                             exdir = tempdir()))[1]

## SELECT QUERY SPECTRA ---
## Decompress the query mzML files that come with MS2ID
queryFile <- system.file("extdata/QRYspectra.zip",
                         package = "MS2ID",
                         mustWork = TRUE)
queryFolder <- file.path(tempdir(), "QRYspectra")
library(utils)
unzip(queryFile, exdir = queryFolder)

## ANNOTATION ---
library(MS2ID)
MS2IDlib <- MS2ID(MS2IDFolder)
annotResult <- annotate(QRYdata = queryFolder, MS2ID = MS2IDlib)

#> Loading query spectra ...
#> Obtaining consensus spectra ...
#> Solving distance metrics between query and reference spectra ...
#> Processing results obtained ...

## Browse visually the results---
if (FALSE) {
MS2IDgui(annotResult)
}