adductQuant: Adduct quantification for adductomicsR

Description Usage Arguments Value Examples

Description

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

Usage

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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

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## 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)

JosieLHayes/adductomicsR documentation built on May 5, 2019, 9:43 p.m.