Export MS/MS spectra for all features

Loop export_MSdev_feature_MSMS over features. Feature IDs are taken from advancedAna$featureRaw, else feature.se, else xcms featureDefinitions (_pos/ _neg suffix). Writes {feature_id}.MSMS.png (experimental vs reference mirror when a reference spectrum is present). Failures on individual features are warned and skipped.

Usage

MSdev_export_feature_MSMS(
  object,
  out.dir = file.path(object@projectInfo$projectDir, "MSMS"),
  feature_id = NULL,
  cpdb_path = object@projectInfo$CompoundDB_path
)

Arguments

object

MSdev object

out.dir

Output directory. Default object@projectInfo$projectDir/MSMS.

feature_id

Optional character vector of feature IDs. Default all features discovered as above.

cpdb_path

Optional path to a CompoundDb SQLite file. Default object@projectInfo$CompoundDB_path (set by MSdev_annotation).

Value

Invisible character vector of feature IDs attempted.

See also

export_MSdev_feature_MSMS, plot_MSdev_feature_spectrum, MSdev_export_feature_Chromatographs