smoothSingleXIC: Smooth chromatogram signal

In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

Smooth chromatogram signal

Description

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.

Usage

smoothSingleXIC(
  chromatogram,
  type,
  samplingTime = NULL,
  kernelLen = NULL,
  polyOrd = NULL
)

Arguments

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.

Details

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

Value

A dataframe with two columns.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL3 Date: 2020-02-21

See Also

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

Examples

data("XIC_QFNNTDIVLLEDFQK_3_DIAlignR")
chrom <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]][[1]]
## Not run: 
newChrom <- smoothSingleXIC(chrom, type = "sgolay", samplingTime = 3.42, kernelLen = 9,
 polyOrd = 3)

## End(Not run)

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.