smoothXICs: Smooth chromatogram signals from a list

Description Usage Arguments Value Author(s) See Also Examples

View source: R/chromatogram_manip.R

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

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smoothXICs(
  XICs,
  type = "none",
  samplingTime = NULL,
  kernelLen = NULL,
  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, shubh.gupta@mail.utoronto.ca

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

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data("XIC_QFNNTDIVLLEDFQK_3_DIAlignR")
XICs <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["run0"]][["14299_QFNNTDIVLLEDFQK/3"]]
## Not run: 
newXICs <- smoothXICs(XICs, type = "sgolay", samplingTime = 3.42, kernelLen = 9,
 polyOrd = 3)

## End(Not run)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.