smoothSpectrum: Smooth Noise in Spectrum

In wesleyburr/subMaldi: Organization and Processing of MALDI-MS Datasets

Description

Offers two different methods for smoothing noise in raw spectral data: a moving average filter and the Savitzky-Golay filter (1).

Usage

smoothSpectrum(
  dat,
  mass_dat,
  intensity_dat,
  method = NULL,
  p = NULL,
  n = NULL,
  m = 0,
  ts = 1
)

Arguments

dat	The name of the spectral data frame, containing m/z data in the first column and spectral intensity data in subsequent columns.
mass_dat	A character string; the name of the column in dat containing the m/z data for the spectrum.
intensity_dat	A character string; the name of the column in dat containing the intensity data for the spectrum to be smoothed.
method	A character string; the method to be used for smoothing. Available methods include a Savitzky-Golay filter ("sgolay") and a moving average filter ("mov_avg.")
p	Single numeric value. If method = "sgolay", the filter order of smoothing. Default = NULL.
n	Single odd numeric value. If method = "sgolay", the length of the smoothing filter. If method = "mov_avg", the window span size. Default = NULL.
m	Single numeric value. If method = "sgolay", returns the m-th derivative of the filter coefficients. Default = 0.
ts	Single numeric value. If method = "sgolay", the time scaling factor. Default = 1.

Value

Returns a new data frame containing the smoothed spectral data.

Author(s)

Kristen Yeh <[e-mail]> Wesley Burr <[e-mail]>

References

https://github.com/wesleyburr/subMaldi (1) A. Savitzky, M.J.E. Golay, Smoothing and differentiation of data by simplified least-squares procedures, Anal. Chem. 36 (8) (1964) 1627-1639.

Examples

## Load sample dataset "Before1.rda"
data("Before1")

## Testing method "sgolay"
# test <- smoothSpectrum(dat = Before1, mass_dat = "mass",
#                       intensity_dat = "Intensity", 
#                       method = "sgolay", p = 4, 
#                       n = 25, m = 0)

## Testing method "mov_avg"                        
# test <- smoothSpectrum(dat = Before1, mass_dat = Before1$mass,
#                       intensity_dat = Before1$Intensity,
#                       method = "mov_avg", n = 25)
#                  

wesleyburr/subMaldi documentation built on Oct. 1, 2021, 7:07 a.m.