R: Baseline Correction of a Spectra Object

baselineSpectra {ChemoSpec} | R Documentation

## Baseline Correction of a Spectra Object

### Description

This function mostly wraps functions in package baseline which carries out a variety of baseline correction routines. A simple linear correction method is also available.

### Usage

    baselineSpectra(spectra, int = TRUE, retC = FALSE, ...)

### Arguments

`spectra` | An object of S3 class `Spectra` to be checked.
`int` | Logical; if `TRUE`, do the correction interactively using widgets. No results are saved. Use this for inspection and exploration only.
`retC` | Logical: shall the baseline-corrected spectra be returned in the `Spectra` object?
`...` | Other arguments passed downstream. The relevant ones can be found in `baseline`. Be sure to pay attention to argument `method` as you will probably want to use it. You can also use `method = "linear"` for a simple linear fit, see Details.

### Details

In plots using methods from the baseline package, the x axis ticks give the data point index, not the original values from your data. Note that you cannot zoom the non-interactive display of corrected spectra because the underlying function hardwires the display. Try the interactive version instead (`int = TRUE`), or use `plotSpectra` on the corrected data. In addition to the methods provided by `baseline`, you can also use `method = "linear"`. This correction is handled locally, and is very simple: a line is drawn from the first data point to the last, and this becomes the new baseline. This is most suitable for cases in which the baseline rises or falls steadily, as is often seen in chromatograms.

### Value

If `int = TRUE`, an interactive plot is created. If `int = FALSE` and `retC = FALSE`, an object of class `baseline` is returned (see `baseline-class`). If `int = FALSE` and `retC = TRUE`, a `Spectra` object containing the corrected spectra is returned. In these latter two cases plots are also drawn.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

https://github.com/bryanhanson/ChemoSpec

### Examples

    data(SrE.IR)
    require("IDPmisc") # needed specifically for rfbaseline
    temp <- baselineSpectra(SrE.IR, int = FALSE, method = "rfbaseline")

[Package ChemoSpec version 4.4.97 Index]