smoothSingleXIC {DIAlignR} | R Documentation |
Smoothing methods are Savitzky-Golay, Boxcar, Gaussian kernel and LOESS. Savitzky-Golay smoothing is good at preserving peak-shape compared to gaussian and boxcar smoothing. However, it assumes equidistant points that fortunately is the case for DIA data. This requires a quadratic memory to store the fit and slower than other smoothing methods.
smoothSingleXIC( chromatogram, type, samplingTime = NULL, kernelLen = NULL, polyOrd = NULL )
chromatogram |
(dataframe) A dataframe of two columns. First column must always be monotonically increasing. |
type |
(char) must be either sgolay, boxcar, gaussian, loess or none. |
samplingTime |
(numeric) Time difference between neighboring points. |
kernelLen |
(integer) Number of data-points to consider in the kernel. |
polyOrd |
(integer) Order of the polynomial to be fit in the kernel. |
Gaussian smoothing uses a gaussian function whose bandwidth is scaled by 0.3706505 to have quartiles at +/- 0.25*bandwidth. The point selection cut-off is also hard at 0.3706505*4*bandwidth.
qnorm(0.75, sd = 0.3706505)
The definition of C_ksmooth can be found using getAnywhere('C_ksmooth') stats:::C_ksmooth
A dataframe with two columns.
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL3 Date: 2020-02-21
https://terpconnect.umd.edu/~toh/spectrum/Smoothing.html, https://rafalab.github.io/dsbook/smoothing.html, https://github.com/SurajGupta/r-source/blob/master/src/library/stats/src/ksmooth.c
data("XIC_QFNNTDIVLLEDFQK_3_DIAlignR") chrom <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["run0"]][["14299_QFNNTDIVLLEDFQK/3"]][[1]] ## Not run: newChrom <- smoothSingleXIC(chrom, type = "sgolay", samplingTime = 3.42, kernelLen = 9, polyOrd = 3) ## End(Not run)