Peak integration for a GCIMSSample

Peak integration for a GCIMSSample

# S4 method for GCIMSSample
integratePeaks(
  object,
  peak_list,
  integration_size_method = c("fixed_size", "free_size"),
  rip_saturation_threshold = 0.1,
  verbose = FALSE
)

Arguments

object

A GCIMSSample object

peak_list

A data frame with the peak list

integration_size_method

If "fixed_size", the ROI integration limits are the same for all the peaks that belong to the same cluster. If "free_size", each ROI has its own integration limits, regardless of the cluster it is assigned to.

rip_saturation_threshold

Used to compute the "Saturation" column. If the ratio of the RIP intensity at the ROI apex with respect to the maximum RIP is below this threshold, the RIP is considered almost depleted, and it's more likely that the ROI suffers from non-linearities.

verbose

If TRUE, debug information will be printed

Value

The modified GCIMSSample, with an updated peak list