normalizeByInternalStandard {Metab} | R Documentation

## Normalize metabolomics data sets by a specific metabolite defined as internal standard.

### Description

In the specified inputData, every metabolite from each sample will be divided by the intensity/abundance of the metabolite defined as internal standard, which is specified through the argument internalStandard.

### Usage

    normalizeByInternalStandard(
    	inputData,
    	internalStandard,
    	save = TRUE,
    	folder,
    	output = "normalizedByInternalStandard"
    )

### 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.
`internalStandard` | A character string indicating the name of the compound to be used as internal standard. If internalStandard is missing, a list of metabolites is presented to the user to interactively choose the correct compound.
`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 string indicating the path to the folder where the results will be saved.
`output` | A character string indicating the name of the .csv file to be generated.

### Details

normalizeByInternalStandard will divide the abundances of each metabolite in a specific sample by the abundance of the chosen internal standard in this specific sample.

### Value

normalizeByInternalStandard generates a data frame containing metabolite abundances normalized by the nominated internal standard.

Note that the first line of the resulting data.frame is used to represent sample meta-data (for example replicates).

### Author(s)

Raphael Aggio <ragg005@aucklanduni.ac.nz>

### 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

### See Also

`htest`, `MetReport`, `MetReportNames`, `normalizeByBiomass`, `removeFalsePositives`, `buildLib`

### Examples

    ### Load the inputData ###
    data(exampleMetReport)
    ### Normalize ####
    normalizedData <- normalizeByInternalStandard(
    	exampleMetReport,
    	internalStandard = "Acetone",
    	save = FALSE
    	)
    ### Show results ####
    print(normalizedData)

[Package Metab version 1.28.0 Index]