normMethod_median: Normalize a Spectral Dataset to its Median Intensity

In wesleyburr/subMaldi: Organization and Processing of MALDI-MS Datasets

Description

Called internally by normSpectra(). Evaluates the median of each spectrum in a dataset after removing 0 values introduced by mapping. If the medians are not equal between spectra, a normalization factor is applied to the spectral intensities until all median intensities in the dataset are equal. Capable of normalizing 2-6 spectra at once.

Usage

norm_median(dat, mass_dat, spectra_cols)

Arguments

dat	The name of the spectral data frame, containing m/z data in the first column and spectral intensity data in subsequent columns.
mass_dat	A character string; the name of the column in dat containing the m/z data for the spectrum.
spectra_cols	A character string; the names of the column in dat containing the intensity data for the spectrs to be analyzed.

Value

Returns a new data frame including the original m/z data and normalized intensity data.

Author(s)

Kristen Yeh <[e-mail]> Wesley Burr <[e-mail]>

References

https://github.com/wesleyburr/subMaldi

See Also

normSpectra

Examples

## Load sample dataset "Master2.rda"
data("Master2")

## Normalize spectra "Before1" and "Before2" to their median intensity
ex <- normSpectra(dat = Master, mass_dat = "full_mz", method = "median", 
            spectra_cols = c("Before1", "Before2"))

wesleyburr/subMaldi documentation built on Oct. 1, 2021, 7:07 a.m.