findPeaks {andurinha} | R Documentation |
This function finds peaks and allows to the most relevant based on the second derivative/absorbance sum spectrum.
findPeaks(
data,
resolution = 4,
minAbs = 0.1,
cutOff = NULL,
scale = TRUE,
ndd = TRUE
)
data |
A data frame object, which contains in the first column the wave numbers and in the following columns the samples absorbances. |
resolution |
The equipment measurement resolution; by default 4 cm-1. |
minAbs |
The cut off value to check spectra quality; by default 0.1. |
cutOff |
The second derivative/absorbance sum spectrum cut off to reduce the raw peaks table; by default NULL. |
scale |
By default (TRUE) the data is scaled by Z-scores. Use FALSE in case you do not want to scale it. |
ndd |
By default (TRUE) the peaks are searched based on the second derivative sum spectrum. Use FALSE in case you want to search them based on the absorbance sum spectrum. |
A list with a collection of data frames which contains:
dataZ: the standardised data by Z-scores.
secondDerivative: the second derivative values of the data.
sumSpectrum_peaksTable: the peaks wave numbers and their second derivative/absorbance sum spectrum values.
peaksTable: the selected peaks wave numbers and their absorbance for each spectrum.
importSpectra
, gOverview
and
plotPeaks
# Find Peaks based on the absorbance sum spectrum
fp.abs <- findPeaks(andurinhaData, ndd = FALSE)
# See the peaks table of the absorbance sum spectrum
fp.abs$sumSpectrum_peaksTable
# Find Peaks based on the second derivative sum spectrum
fp.ndd <- findPeaks(andurinhaData)
# See the peaks table of the second derivative sum spectrum
fp.ndd$sumSpectrum_peaksTable
# Select a cutOff to reduce the number of peaks in the table
# (i.e. select the most relevant)
# fp.ndd$sumSpectrum_peaksTable %>%
# arrange(desc(sumSpectrum))
# Run findPeaks() with the new cutOff
fp.ndd2 <- findPeaks(andurinhaData, cutOff = 0.25)