specNoise: Calculate noise for a sparse continuum mass spectrum
In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis
View source: R/functions-xcmsRaw.R
specNoise R Documentation
Calculate noise for a sparse continuum mass spectrum
Description
Given a sparse continuum mass spectrum, determine regions where
no signal is present, substituting half of the minimum intensity
for those regions. Calculate the noise level as the weighted mean
of the regions with signal and the regions without signal.
If there is only one raw peak, return zero.
Usage
specNoise(spec, gap = quantile(diff(spec[, "mz"]), 0.9))
Arguments
spec
matrix with named columns mz and intensity
gap
threshold above which to data points are considerd to be separated
by a blank region and not bridged by an interpolating line
Details
The default gap value is determined from the 90th percentile of
the pair-wise differences between adjacent mass values.
Value
A numeric noise level
Author(s)
Colin A. Smith, csmith@scripps.edu
See Also
getSpec,
specPeaks
xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.
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View source: R/functions-xcmsRaw.R
| specNoise | R Documentation |
Calculate noise for a sparse continuum mass spectrum
Description
Given a sparse continuum mass spectrum, determine regions where no signal is present, substituting half of the minimum intensity for those regions. Calculate the noise level as the weighted mean of the regions with signal and the regions without signal. If there is only one raw peak, return zero.
Usage
specNoise(spec, gap = quantile(diff(spec[, "mz"]), 0.9))
Arguments
spec |
matrix with named columns |
gap |
threshold above which to data points are considerd to be separated by a blank region and not bridged by an interpolating line |
Details
The default gap value is determined from the 90th percentile of the pair-wise differences between adjacent mass values.
Value
A numeric noise level
Author(s)
Colin A. Smith, csmith@scripps.edu
See Also
getSpec,
specPeaks
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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