smoothXICs: Smooth chromatogram signals from a list

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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

smoothXICs(
  XICs,
  type = "none",
  samplingTime = NULL,
  kernelLen = 9L,
  polyOrd = NULL
)

Arguments

XICs	(A list) A list of dataframe that consists of two columns. First column must 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.

Value

A list.

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

Examples

data("XIC_QFNNTDIVLLEDFQK_3_DIAlignR")
XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt"]][["4618"]]
newXICs <- smoothXICs(XICs, type = "sgolay", samplingTime = 3.42, kernelLen = 9,
 polyOrd = 3)

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.