metaXpara-class: An S4 class to represent the parameters and data for data...
In wenbostar/metaX: A flexible and comprehensive software for processing omics data.
metaXpara-class R Documentation
An S4 class to represent the parameters and data for data processing
Description
An S4 class to represent the parameters and data for data processing
Arguments
para
A metaXpara object
value
New value
Value
A object of metaXpara
Slots
dir.caseThe path names of the NetCDF/mzXML files to read
dir.ctrlThe path names of the NetCDF/mzXML files to read
sampleListFileThe file name of containing the experiment design
sampleListA data.frame containing the experiment design
ratioPairsA character containing the ratio pairs, such as "A:B;A:C"
pairTestPaired test, default is FALSE
missValueImputeMethodA character of missing value imputation method
sampleListHeadThe name of head of sampleListFile
outdirThe output directory
prefixThe prefix of output file
xcmsPeakListFileThe file of output from XCMS
figA list of file names of figures
peaksDataA data.frame containing the peaks data
VIPA data.frame containing the VIP
rawPeaksA data.frame containg the raw peaks data
xcmsSetObjAn object of xcmsSet
quantA data.frame containing the quantification result
idresA data.frame containing the identification result
xcmsSet.methodMethod to use for peak detection. See details
findPeaks in package XCMS
xcmsSet.ppmThe maxmial tolerated m/z deviation in consecutive scans,
in ppm (parts per million)
xcmsSet.peakwidthChromatographic peak width, given as
range (min,max) in seconds
xcmsSet.snthreshThe signal to noise ratio cutoff, definition see
findPeaks.centWave
xcmsSet.prefilterprefilter=c(k,I),
see findPeaks.centWave
xcmsSet.mzCenterFunSee findPeaks.centWave
xcmsSet.integrateSee findPeaks.centWave
xcmsSet.mzdiffSee findPeaks.centWave
xcmsSet.noiseSee findPeaks.centWave
xcmsSet.verbose.columnsSee findPeaks.centWave
xcmsSet.polarityFilter raw data for positive/negative scans.
See xcmsSet
xcmsSet.profparamParameters to use for profile generation.
See xcmsSet
xcmsSet.nSlavesThe number of slaves/cores to be used for parallel
peak detection. See xcmsSet
xcmsSet.fitgaussSee findPeaks.centWave
xcmsSet.sleepThe number of seconds to pause between plotting
peak finding cycles. See findPeaks.centWave
xcmsSet.fwhmSee findPeaks.matchedFilter
xcmsSet.maxSee findPeaks.matchedFilter
xcmsSet.stepSee findPeaks.matchedFilter
group.bw0See group.density
group.mzwid0See group.density
group.bwSee group.density
group.mzwidSee group.density
group.minfracSee group.density
group.minsampSee group.density
group.maxSee group.density
group.sleepSee group.density
retcor.methodSee retcor
retcor.profStepSee retcor.obiwarp
retcor.plottypeSee retcor.obiwarp
qcRlscSpanThe value of span for QC-RLSC
Author(s)
Bo Wen wenbostar@gmail.com
wenbostar/metaX documentation built on July 4, 2023, 7:50 p.m.
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| metaXpara-class | R Documentation |
An S4 class to represent the parameters and data for data processing
Description
An S4 class to represent the parameters and data for data processing
Arguments
para |
A metaXpara object |
value |
New value |
Value
A object of metaXpara
Slots
dir.caseThe path names of the NetCDF/mzXML files to read
dir.ctrlThe path names of the NetCDF/mzXML files to read
sampleListFileThe file name of containing the experiment design
sampleListA data.frame containing the experiment design
ratioPairsA character containing the ratio pairs, such as "A:B;A:C"
pairTestPaired test, default is FALSE
missValueImputeMethodA character of missing value imputation method
sampleListHeadThe name of head of
sampleListFileoutdirThe output directory
prefixThe prefix of output file
xcmsPeakListFileThe file of output from XCMS
figA
listof file names of figurespeaksDataA
data.framecontaining the peaks dataVIPA
data.framecontaining the VIPrawPeaksA
data.framecontaing the raw peaks dataxcmsSetObjAn object of
xcmsSetquantA
data.framecontaining the quantification resultidresA
data.framecontaining the identification resultxcmsSet.methodMethod to use for peak detection. See details
findPeaksin package XCMSxcmsSet.ppmThe maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million)
xcmsSet.peakwidthChromatographic peak width, given as range (min,max) in seconds
xcmsSet.snthreshThe signal to noise ratio cutoff, definition see
findPeaks.centWavexcmsSet.prefilterprefilter=c(k,I), see
findPeaks.centWavexcmsSet.mzCenterFunSee
findPeaks.centWavexcmsSet.integrateSee
findPeaks.centWavexcmsSet.mzdiffSee
findPeaks.centWavexcmsSet.noiseSee
findPeaks.centWavexcmsSet.verbose.columnsSee
findPeaks.centWavexcmsSet.polarityFilter raw data for positive/negative scans. See
xcmsSetxcmsSet.profparamParameters to use for profile generation. See
xcmsSetxcmsSet.nSlavesThe number of slaves/cores to be used for parallel peak detection. See
xcmsSetxcmsSet.fitgaussSee
findPeaks.centWavexcmsSet.sleepThe number of seconds to pause between plotting peak finding cycles. See
findPeaks.centWavexcmsSet.fwhmSee
findPeaks.matchedFilterxcmsSet.maxSee
findPeaks.matchedFilterxcmsSet.stepSee
findPeaks.matchedFiltergroup.bw0See
group.densitygroup.mzwid0See
group.densitygroup.bwSee
group.densitygroup.mzwidSee
group.densitygroup.minfracSee
group.densitygroup.minsampSee
group.densitygroup.maxSee
group.densitygroup.sleepSee
group.densityretcor.methodSee
retcorretcor.profStepSee
retcor.obiwarpretcor.plottypeSee
retcor.obiwarpqcRlscSpanThe value of span for QC-RLSC
Author(s)
Bo Wen wenbostar@gmail.com
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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