Peak list: Create an accepted column based on some criteria

Source: R/area_estimation.R

Peak list: Create an accepted column based on some criteria

peaklist_accept_peaks(
  peak_data,
  nmr_dataset,
  nrmse_max = Inf,
  area_min = 0,
  area_max = Inf,
  ppm_min = -Inf,
  ppm_max = Inf,
  keep_rejected = TRUE,
  verbose = FALSE
)

Arguments

peak_data

The peak list (a data frame)

nmr_dataset

The nmr_dataset where the peak_data was computed from

nrmse_max

The normalized root mean squared error of the lorentzian peak fitting must be less than or equal to this value

area_min

Peak areas must be larger or equal to this value

area_max

Peak areas must be smaller or equal to this value

ppm_min

The peak apex must be above this value

ppm_max

The peak apex must be below this value

keep_rejected

If FALSE, removes those peaks that do not satisfy the criteria and remove the accepted column (since all would be accepted)

verbose

Print informational message

Value

The peak_data, with a new accepted column (or maybe some filtered rows)

Examples

# Fake data:
nmr_dataset <- new_nmr_dataset_1D(
    1:10,
    matrix(c(1:5, 4:2, 3, 0), nrow = 1),
    list(external = data.frame(NMRExperiment = "10"))
)
peak_data <- data.frame(
    peak_id = c("Peak1", "Peak2"),
    NMRExperiment = c("10", "10"),
    ppm = c(5, 9),
    pos = c(5, 9),
    intensity = c(5, 3),
    ppm_infl_min = c(3, 8),
    ppm_infl_max = c(7, 10),
    gamma_ppb = c(1, 1),
    area = c(25, 3),
    norm_rmse = c(0.01, 0.8)
)
# Create the accepted column:
peak_data <- peaklist_accept_peaks(peak_data, nmr_dataset, area_min = 10, keep_rejected = FALSE)
stopifnot(identical(peak_data$peak_id, "Peak1"))