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Excise Chemical Shift Regions from 1D NMR Spectra

Source: R/preproc_excise.R
excise.Rd

Removes specified chemical shift regions from 1D \(^1\)H NMR spectra. By default, commonly excluded metabolomics regions are removed (upfield/downfield noise, water, urea).

Usage

excise(x, ppm = NULL, regions = NULL)

Arguments

x

Numeric matrix or vector. Spectra in rows and variables in columns.

ppm

Numeric vector of chemical shift positions (ppm). If omitted, ppm is inferred from colnames(X).

regions

Named list of numeric vectors (length 2), specifying ppm regions to remove. Each element must define lower and upper bounds.

Value

Numeric matrix with specified chemical shift regions removed.

Details

Default regions removed (ppm):

  • Upfield noise: [min(ppm), 0.25]

  • Residual water: [4.5, 5.2]

  • Urea region: [5.5, 6.0]

  • Downfield noise: [9.7, max(ppm)]

Removed regions are recorded in attr(X, "m8_prep") if present. Updated ppm values are stored in column names and in attr(X, "m8_axis")$ppm.

Examples

set.seed(1)
ppm <- seq(0, 10, length.out = 1000)
X <- matrix(rnorm(100 * length(ppm)), nrow = 100)

Xe <- excise(X, ppm)

dim(Xe)
#> [1] 100 825
names(attributes(Xe))
#> [1] "dim"      "dimnames" "m8_axis"  "m8_prep"