normalizeByBiomass: A function to normalize metabolomics data by the biomass associated to each biological sample (e.g. cell number or O.D.)

Description

normalizeByBiomass divides the intensity of each metabolite in a specific sample by the value of the biomass measured for this specific sample.

Usage

normalizeByBiomass(inputData, biomass, save = TRUE, folder, output = "norm_bio")

Arguments

inputData

When inputData is missing, a dialog box will pop up allowing the user to click-and-point to the .csv file from which the data is to be read. It may also receive a character string pointing to a .csv file containing a data frame such as data(exampleMetReport), generated by MetReport. Alternatively, inputData takes an R vector containing the desired data frame.

biomass

When biomass is missing, a dialog box will pop up allowing the user to click-and-point to the .csv file from which the biomasses are to be read (See data(exampleBiomass)). It may also receive a character string pointing to a .csv file containing a data frame such as data(exampleBiomass). Alternativelly, it may receive a character vector indicating the data frame such as data(exampleBiomass).

save

A logical vector (TRUE or FALSE) indicating if the resultant data frame should be saved in a .csv file. If save = TRUE, the .csv file will be saved in the path defined in the argument folder.

folder

A character vector indicating the path to the folder where the results will be saved.

output

A character vector indicating the name of the .csv file to be generated.

Value

norm.biomass produces a data frame normalized by biomass.Note that the first line of the resulting data.frame is used to represent sample meta-data (for example replicates).

Details

normalizeByBiomass loads the inputData and searches the data frame Biomass for the values of the biomasses associated with each sample present in the inputData. When the value is found, the abundances of metabolites associated with each sample is divided by the value of its respective biomass.

References

Aggio, R., Villas-Boas, S. G., & Ruggiero, K. (2011). Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS. Bioinformatics, 27(16), 2316-2318. doi: 10.1093/bioinformatics/btr379

Examples

Run this code

### Load the inputData ###
data(exampleMetReport)
### Load the list of biomasses ### 
data(exampleBiomass)
### Normalize ####
normalizedData <- normalizeByBiomass(exampleMetReport, biomass = exampleBiomass, save = FALSE)
### Show results ###
print(normalizedData)

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