peak picking {rNMR} | R Documentation |
Peak picking functions.
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, ...)
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 ). |
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.
pa
paAll
pw
pwAll
pReg
pm
ph
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
pDelAll
pe
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
rp
rpAll
Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
ct
for changing plot settings; roi
for
creating ROIs; import
for importing/exporting rNMR peak
lists; ed
for extracting data from rNMR peak lists;
rNMR
for other rNMR help topics.