R: rNMR peak picking utilities

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

rNMR peak picking utilities

Description

Usage

Arguments

Details

Value

Author(s)

See Also