adductQuant: Adduct quantification for adductomicsR
In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

Description Usage Arguments Value Examples

reads mzXML files from a directory, corrects RT according to RT correction model and quantifies peaks.

adductQuant(nCores = NULL, targTable = NULL, 
intStdRtDrift = NULL, rtDevModels = NULL, 
filePaths = NULL, quantObject = NULL, indivAdduct = NULL, maxPpm = 4,
minSimScore = 0.8, spikeScans = 2, minPeakHeight = 100, maxRtDrift = 20,
maxRtWindow = 120, isoWindow = 80, 
hkPeptide = "LVNEVTEFAK", gaussAlpha = 16)

`nCores`	number of cores to use for analysis. If NULL then 1 core will be used.
`targTable`	is the fullpath to the target table. See inst/extdata/examplePeptideTargetTable.csv for an example.
`intStdRtDrift`	the maximum drift for the internal standard in seconds. Default = NULL and therefore no RT correction is applied to the internal standard.
`rtDevModels`	is the full path to the rtDevModels.RData file from rtDevModels(). default is NULL and therefore has no RT correction.
`filePaths`	required list of mzXML files for analysis. If all files are in the same directory these can be accessed using list.files('J:\parentdirectory\directoryContainingfiles', pattern='.mzXML', all.files=FALSE, full.names=TRUE).
`quantObject`	character string for filepath to an AdductQuantif object to be integrated.
`indivAdduct`	numeric vector of AdductQuantif targets to re-integrate
`maxPpm`	numeric for the maximum parts per million to be used.
`minSimScore`	a numeric between 0
`spikeScans`	a numeric for the number of scans that a spike must be seen in for it to be integrated. Default is 2.
`minPeakHeight`	numeric to determine the minimum height for a peak to be integrated. Default is set low at 100.
`maxRtDrift`	numeric for the maximum retention time drift to be considered. Default is 20.
`maxRtWindow`	numeric in seconds for the retention time window (total window will be 2 times this value)
`isoWindow`	numeric for the pepide isotope window in seconds, default is 80
`hkPeptide`	is capitalized string for the housekeeping peptide. The default is 'LVNEVTEFAK' from human serum albumin.
`gaussAlpha`	numeric for the gaussian smoothing parameter to smooth the peaks. Default is 16. Output is an adductQuantf object saved to the working directory

adductQuant object

## Not run: 
eh = ExperimentHub();
temp = query(eh, 'adductData');
adductQuant(nCores=2, targTable=paste0(system.file("extdata", 
package = "adductomicsR"),'/exampletargTable2.csv'), intStdRtDrift=30, 
rtDevModels=paste0(hubCache(temp),"/rtDevModels.RData"),
filePaths=list.files(hubCache(temp),pattern=".mzXML", all.files=FALSE,
full.names=TRUE)[1],quantObject=NULL,
indivAdduct=NULL,maxPpm=5,minSimScore=0.8,spikeScans=1,
minPeakHeight=100,maxRtDrift=20,maxRtWindow=240,isoWindow=80,
hkPeptide='LVNEVTEFAK', gaussAlpha=16)

## End(Not run)