pickUtils {rNMR}R Documentation

rNMR peak picking utilities

Description

Utilities used for or related to peak picking in rNMR.

Usage

appendPeak(newList, oldList)
isNoise(x, data, thresh = -0.15)
localMax(x, thresh, noiseFilt)
matchShift(inFolder = fileFolder[[wc()]], w1 = NULL, w2 = NULL, w1.pad = 0, 
	w2.pad = 0, invert = FALSE, return.inc = FALSE, return.seq = FALSE,
	overRange = FALSE)
maxShift(inFile, invert = FALSE, conDisp = c(TRUE, TRUE), massCenter = FALSE)
pdisp(col, cex, pch, pos, offset, ...)
peakPick(fileName = currentSpectrum, inFile = NULL, w1Range = NULL, 
	w2Range = NULL, append = FALSE, internal = FALSE, ...)
peakPick1D(fileName = currentSpectrum, inFile = NULL, w2Range = NULL, 
	w2Gran = 2, noiseFilt = globalSettings$peak.noiseFilt, maxOnly = FALSE, ...)
peakPick2D(fileName = currentSpectrum, inFile = NULL, w1Range = NULL, 
	w2Range = NULL, fancy = FALSE, noiseFilt = globalSettings$peak.noiseFilt, 
	maxOnly = FALSE, ...)
peakVolume(inFile, gran = 200, c.vol = FALSE, baselineCorr = FALSE)
regionMax(fileName = currentSpectrum, redraw = TRUE, noiseCheck = TRUE)
shiftToROI(shiftList = NULL, w1Delta = 1, w2Delta = 0.05)

Arguments

newList data.frame; peak list to append.
oldList data.frame; peak list to be appended.
x numeric; a candidate signal (isNoise) or a matrix containing the range of data being analyzed (localMax).
data numeric vector; the field of data being tested.
thresh numeric; noise threshold. For isNoise, values can range from 0 (no filtering) to -1 (no data returned). For localMax, this indicates the minimum level to be included.
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), 2 applies a strong filter (all adjacent points must be above the noise threshold).
inFolder File and graphics parameters for desired spectra as listed in fileFolder.
w1 numeric (vector); w1 chemical shifts to be matched.
w2 numeric (vector); w2 chemical shifts to be matched.
w1.pad integer; number of adjacent points to return in addition to the matched shifts in the indirect dimension.
w2.pad integer; number of adjacent points to return in addition to the matched shifts in the direct dimension.
invert logical; if TRUE, shifts are inverted (reflected across the center of the spectrum) before being returned. R plots must be sorted by increasing x and y values. To meet this requirement all NMR data is inverted before plotting.
return.inc logical; if TRUE, returns the index for the shift as a point in the data matrix, if FALSE, returns the chemical shift.
return.seq logical; if TRUE, returns the entire sequence of shifts covered by the w1 and w2 ranges provided, if FALSE returns the range for the matched shifts.
overRange logical; TRUE returns NA if shifts are outside the spectral window; FALSE returns the closest match to the shifts provided.
conDisp logical vector; c(TRUE, TRUE) returns the chemical shift at the absolute maximum intensity, c(TRUE, FALSE) returns the chemical shift at the maximum intensity, c(TRUE, FALSE) returns the chemical shift at the minimum intensity.
massCenter logical; if TRUE, returns the geometric center for the data, if FALSE, returns shifts at the max/min signal observed.
col character string; color for peak markers, see colors for the many color options.
cex numeric; symbol expansion, see points.
pch numeric or character; symbol used for peak markers, see points.
pos numeric; specifies position for peak label text, see text.
offset numeric; peak label offset, see text.
... Additional graphics (pdisp, see points) or peak picking arguments (see addArg).
fileName character string or vector; spectrum name(s) as they appear in fileFolder.
inFile list; file parameters and data for file being analyzed, the output from the main plot window for the ed function.
w1Range numeric; w1 chemical shift range (c(downfield,upfield)) to be used.
w2Range numeric; w2 chemical shift range (c(downfield,upfield)) to be used.
append logical; if TRUE, appends peaks to the previous list.
internal logical; if TRUE, returns the list without assigning it to fileFolder, if FALSE, assigns the list to fileFolder.
w2Gran integer; granularity of search space used for finding local maxima, smaller values are more exhaustive, bigger values suppress noise.
fancy logical; if FALSE, implements a basic peak picker that returns local maxima only, this is fastest; if TRUE, determines chemical shifts of peaks, groups multiplets, and measures line width and volume.
gran integer; granularity of contour fitting.
maxOnly logical; if TRUE, only the maximum peak is returned.
c.vol logical; if TRUE, returns stacked ellipsoid volumes, if FALSE returns the sum of the visible data (recommended).
baselineCorr logical; performs local baseline correction for 1D spectra if TRUE.
redraw logical; if TRUE, the spectrum is refreshed before exiting.
noiseCheck logical; if TRUE, peak is not returned if its intensity is below the noise threshold (as specified by the thres.1D parameter in globalSettings for 1D spectra or by the contour level settings for 2D spectra).
shiftList data.frame; chemical shift table containing an w1 and an w2 column. A column named "Code" or "Assignment" will be used for the ROI names if present.
w1Delta numeric; width of the desired ROI in the w1 dimension.
w2Delta numeric; width of the ROI in the w2 dimension.

Details

appendPeak
Combines two peak lists. The only requirement is that each peak list must contain "w1", "w2", and "Height" columns.
isNoise
A simple filter for detecting noise signals in 1D data. This function is an obvious area for future improvement, as the filter currently excludes broad signals.
localMax
Finds points in a matrix that are larger than all surrounding points, useful for peak picking algorithms.
matchShift
Looks in the provided spectrum for the closest matches (actual chemical shifts) to the chemical shifts provided. If more than one shift is provided, the function returns the shifts matched over the range of given shifts.
maxShift
Finds the chemical shifts at the maximum, absolute maximum, or minimum intensity for the data provided.
peakPick
Wrapper function for implementing 1D and 2D peak picking in rNMR.
pdisp
Displays the peak list for the current spectrum. Note that this function does not turn the peak display on, so peaks will only be displayed until the next plot refresh.
peakPick1D
1D peak picking algorithm utilizing local maxima (hill climbing method).
peakPick2D
2D peak picking algorithm utilizing local maxima (hill climbing method).
peakVolume
Estimates volumes of 2D peaks using the sum of the visible data or stacked ellipsoids.
regionMax
Finds the chemical shifts at the absolute maximum intensity within a region defined by the user interactively.
shiftToROI
Converts a peak list to an roiTable. See roi for more information on ROIs.

Value

appendPeak returns the newly appended peak list.
isNoise returns TRUE if the data provided is determined to be noise.
localMax returns a vector of points defining the local maxima.
matchShift returns the range of chemical shifts, or indices, for the closest matching w1 and w2 shifts found in a spectrum.
maxShift returns the chemical shifts for the max/min intensity.
peakPick returns a new peak list for the w1/w2 ranges provided.
peakPick1D returns a new peak list for the w2 range provided.
peakPick2D returns a new peak list for the w1/w2 ranges provided.
peakVolume returns volume for 2D peaks and area of 1D peaks.
regionMax returns the chemical shifts for the absolute maximum intensity within the designated region.
shiftToROI returns an roiTable.

Author(s)

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

See Also

toolkit for other rNMR utility functions.


[Package rNMR version 1.1.7 Index]