Skip to contents

MassSpecSettings_SuspectScreening_patRoon

Source: R/class_S3_MassSpecSettings.R
MassSpecSettings_SuspectScreening_patRoon.Rd

Settings for performing suspect screening using the function screenSuspects from the patRoon R package.

Usage

MassSpecSettings_SuspectScreening_patRoon(
  suspects = NULL,
  rtWindow = 12,
  mzWindow = 0.005,
  filtered = FALSE
)

Arguments

suspects

A data.frame with suspect information. See section Suspect list format in screenSuspects for more information.

rtWindow

The retention time window (in seconds) that will be used for matching a suspect (+/- feature data).

mzWindow

The m/z window that will be used for matching a suspect (+/- feature data)..

filtered

Logical (length 1). When TRUE, filtered features/groups are considered.

Value

A ProcessingSettings S3 class object with subclass MassSpecSettings_SuspectScreening_patRoon.

References

Helmus R, ter Laak TL, van Wezel AP, de Voogt P, Schymanski EL (2021). “patRoon: open source software platform for environmental mass spectrometry based non-target screening.” Journal of Cheminformatics, 13(1). doi:10.1186/s13321-020-00477-w .

Helmus R, van de Velde B, Brunner AM, ter Laak TL, van Wezel AP, Schymanski EL (2022). “patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening.” Journal of Open Source Software, 7(71), 4029. doi:10.21105/joss.04029 .