normalizeByInternalStandard {Metab} | R Documentation |
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.
normalizeByInternalStandard( inputData, internalStandard, save = TRUE, folder, output = "normalizedByInternalStandard" )
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 |
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. |
normalizeByInternalStandard will divide the abundances of each metabolite in a specific sample by the abundance of the chosen internal standard in this specific sample.
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).
Raphael Aggio <ragg005@aucklanduni.ac.nz>
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
htest
,
MetReport
,
MetReportNames
,
normalizeByBiomass
,
removeFalsePositives
,
buildLib
### Load the inputData ### data(exampleMetReport) ### Normalize #### normalizedData <- normalizeByInternalStandard( exampleMetReport, internalStandard = "Acetone", save = FALSE ) ### Show results #### print(normalizedData)