R: Peak picking

peak picking {rNMR}

R Documentation

Peak picking

Description

Peak picking functions.

Usage

pp()
pa(...)
paAll(...)
pw(append = TRUE, ...)
pwAll(append = TRUE, ...)
pReg(fileName = currentSpectrum, append = TRUE, ...)
pm(fileName = currentSpectrum, append = TRUE, ...)
ph(forcePoint = FALSE)
pDel()
pDelAll()
pe(table)
pv()
nf(noiseFilt)
rp(fileName = currentSpectrum, append = TRUE, parent = NULL, ...)
rpAll(append = TRUE, ...)

Arguments

`append`	logical; `TRUE` appends new peaks to the previous list.
`fileName`	character string or vector; spectrum name(s) as they appear in fileFolder, defaults to the current spectrum.
`forcePoint`	logical; when `TRUE`, the intensity and chemical shifts will be taken from the closest data point in the spectrum; when `FALSE` the intensity is taken from the closest data point but chemical shifts will not be corrected to match the spectrum.
`table`	data.frame; a peak table to edit.
`noiseFilt`	integer; either `0`, `1` or `2`. `0` does not apply a noise filter, `1` applies a mild filter (adjacent points in the direct dimension must be above the noise threshold), and `2` applies a strong filter (all adjacent points must be above the noise threshold).
`parent`	optional Tk toplevel object to set as a parent window for the newly created dialog. If provided, the dialog will appear near its parent and will bring the parent toplevel object to the front. This is particularly useful for displaying message or error dialogs in response to user interactions within rNMR GUIs.
`...`	Additional arguments can be passed to internal peak picking functions (see `addArg`).

Details

pp displays a peak picking GUI. Changes are only applied to files selected from the files list. Double-clicking on a file name within the files list will switch the current spectrum to the file selected. The noise filter options call on the nf function detailed below. The 1D threshold option must be a numeric value indicating the number of standard deviations away from the noise to set as the minimum peak pick threshold in 1D spectra. Changes made to the 1D threshold are not saved until the Apply button is pressed. This option is not required for 2D spectra, as the peak picking threshold is determined by the displayed contour level(see ct). The Full, Region, ROI, Hand, Edit list, and Clear list buttons call the pa, pReg, rp, ph, pe, and pDel functions, respectively. These functions are detailed below. Peak lists may be imported, exported, or uploaded to the MMCD (Madison Metabolomics Consortium Database, see mmcd) using the Import, Export, and MMCD buttons, respectively.

Shortcut functions

pa: Peak picks the entire spectrum.
paAll: Peak picks the full chemical shift range in all open spectra.
pw: Peak picks the chemical shift range displayed in the main plot window.
pwAll: Peak picks the chemical shift range displayed in the main plot window in all open spectra.
pReg: Peak picks a user designated region.
pm: Peak picks the maximum intensity found within a designated region defined interactively by the in the main plot window.
ph: Manual peak picking; Peak markers are placed by clicking on a point within the main plot window. By default, forcePoint is set to FALSE and markers are placed at the exact cursor location when clicked. To exit manual peak picking mode, right-click in the main plot window.
pDel: Clears picked peaks from the current spectrum.
pDelAll: Clears picked peaks in all open spectra.
pe: Allows the current spectrum's peak list to be edited using rNMR's tableEdit function. If the table argument is provided, this table will be edited and returned, the peak list for the current spectrum will not be affected. See import for more information on peak list structure.
pv: Turns the peak display on and off.
rp: Peak picks inside or outside existing ROI's in the current spectrum.
rpAll: Peak picks existing ROI's in all open spectra.

Author(s)

Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu