adductQuant {adductomicsR} | R Documentation

## Adduct quantification for adductomicsR

### Description

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

### Usage

    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)

### Arguments

`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

### Value

adductQuant object

### Examples

    ## 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)

[Package adductomicsR version 1.4.0 Index]