Normalize a Spectral Dataset to its Median Intensity

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.

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.

References

https://github.com/wesleyburr/subMaldi

Author

Kristen Yeh <kristenyeh@trentu.ca> Wesley Burr <wesleyburr@trentu.ca>

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"))