normMethod_quantile: Normalize Distribution of Intensities

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

Description

Called internally by normSpectra(). Normalizes the distributions of the values in each spectrum in a set. Sorts the intensity data of each spectrum and evaluates the average intensity for each rank. The intensity values are then replaces with the averaged intensities, rearranged in their original order. Capable of analyzing 2-6 spectra at once.

Usage

norm_quantile(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

Examples

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

## Normalize the spectra "Before1" and "Before2"
# using the quantile method
ex <- normSpectra(dat = Master, mass_dat = "full_mz", method = "quantile",
                  spectra_cols = c("Before1", "Before2"))

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