MassSpecSettings_LoadFeaturesMS1_StreamFind

Settings for loading MS1 spectra for features.

Usage

MassSpecSettings_LoadFeaturesMS1_StreamFind(
  rtWindow = c(-2, 2),
  mzWindow = c(-1, 6),
  mzClust = 0.005,
  presence = 0.8,
  minIntensity = 250,
  filtered = FALSE
)

Arguments

rtWindow

Numeric (length 2) with the retention time values (in seconds) for expanding left and right the retention time range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.

mzWindow

Numeric (length 2) with the mass or mass-to-charge ratio (m/z) values (in Da) for expanding left and right the mass range. The first element expands left and the second expands right. Note that the first element should be negative to expand to the left.

mzClust

Numeric (length 1) with the mass deviation threshold (in Da) to cluster mass traces. Highly dependent on the mass resolution of the MS data.

presence

Numeric (length 1) with the required presence ratio from 0 (i.e., doesn't need to be present in any spectra) to 1 (i.e., must be present in all spectra) for traces during clustering of spectra.

minIntensity

Numeric (length 1) with the minimum intensity.

filtered

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

Value

A ProcessingSettings S3 class object with subclass MassSpecSettings_LoadFeaturesMS1_StreamFind.