R/nmr_detect_peaks_align.R
nmr_detect_peaks_tune_snr.Rd
Diagnose SNR threshold in peak detection
nmr_detect_peaks_tune_snr(
ds,
NMRExperiment = NULL,
SNR_thresholds = seq(from = 2, to = 6, by = 0.1),
...
)
An nmr_dataset_1D dataset
A string with the single NMRExperiment used explore the SNR thresholds. If not given, use the first one.
A numeric vector with the SNR thresholds to explore
Arguments passed on to nmr_detect_peaks
nmr_dataset
An nmr_dataset_1D.
nDivRange_ppm
Segment size, in ppms, to divide the spectra and search for peaks.
baselineThresh
All peaks with intensities below the thresholds are excluded. Either:
A numeric vector of length the number of samples. Each number is a threshold for that sample
A single number. All samples use this number as baseline threshold.
NULL
. If that's the case, a default function is used (nmr_baseline_threshold()
)
range_without_peaks
A numeric vector of length two with a region without peaks, only used when baselineThresh = NULL
fit_lorentzians
If TRUE
, fit a lorentzian to each detected peak, to infer its inflection points. For now disabled for backwards compatibility.
verbose
Logical (TRUE
or FALSE
). Show informational messages, such as the estimated baseline
scales
The parameter of peakDetectionCWT function of MassSpecWavelet package, look it up in the original function.
SNR.Th
The parameter of peakDetectionCWT function of MassSpecWavelet package, look it up in the original function. If you set -1, the function will itself re-compute this value.
A list with the following elements:
peaks_detected
: A data frame with the columns from the nmr_detect_peaks output and an additional column
SNR_threshold
with the threshold used on each row.
num_peaks_per_region
: A summary of the peaks_detected
table, with the number of peaks detected on
each chemical shift region
plot_num_peaks_per_region
: A visual representation of num_peaks_per_region
plot_spectrum_and_detections
: A visual representation of the spectrum and the peaks detected with each
SNR threshold. Use plotly::ggplotly or plot_interactive on this to zoom and explore the results.
nmr_detect_peaks
Other peak detection functions:
Pipelines
,
nmr_baseline_threshold()
,
nmr_detect_peaks_plot_overview()
,
nmr_detect_peaks_plot()
,
nmr_detect_peaks()
,
nmr_identify_regions_blood()
,
nmr_identify_regions_cell()
,
nmr_identify_regions_urine()
,
nmr_integrate_regions()