pickUtils {rNMR} | R Documentation |
Utilities used for or related to peak picking in rNMR.
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)
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. |
appendPeak
isNoise
localMax
matchShift
maxShift
peakPick
pdisp
peakPick1D
peakPick2D
peakVolume
regionMax
shiftToROI
roiTable
.
See roi
for more information on ROIs.
|
returns the newly appended peak list. |
|
returns TRUE if the data provided is determined
to be noise. |
|
returns a vector of points defining the local maxima. |
|
returns the range of chemical shifts, or indices, for the closest matching w1 and w2 shifts found in a spectrum. |
|
returns the chemical shifts for the max/min intensity. |
|
returns a new peak list for the w1/w2 ranges provided. |
|
returns a new peak list for the w2 range provided. |
|
returns a new peak list for the w1/w2 ranges provided. |
|
returns volume for 2D peaks and area of 1D peaks. |
|
returns the chemical shifts for the absolute maximum intensity within the designated region. |
|
returns an roiTable . |
Ian A. Lewis ialewis@nmrfam.wisc.edu, Seth C. Schommer schommer@nmrfam.wisc.edu
toolkit
for other rNMR utility functions.