metaXpara-class: An S4 class to represent the parameters and data for data...

Description Arguments Value Slots Author(s)

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.case

The path names of the NetCDF/mzXML files to read

dir.ctrl

The path names of the NetCDF/mzXML files to read

sampleListFile

The file name of containing the experiment design

sampleList

A data.frame containing the experiment design

ratioPairs

A character containing the ratio pairs, such as "A:B;A:C"

missValueImputeMethod

A character of missing value imputation method

sampleListHead

The name of head of sampleListFile

outdir

The output directory

prefix

The prefix of output file

xcmsPeakListFile

The file of output from XCMS

fig

A list of file names of figures

peaksData

A data.frame containing the peaks data

VIP

A data.frame containing the VIP

rawPeaks

A data.frame containg the raw peaks data

xcmsSetObj

An object of xcmsSet

quant

A data.frame containing the quantification result

idres

A data.frame containing the identification result

xcmsSet.method

Method to use for peak detection. See details findPeaks in package XCMS

xcmsSet.ppm

The maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million)

xcmsSet.peakwidth

Chromatographic peak width, given as range (min,max) in seconds

xcmsSet.snthresh

The signal to noise ratio cutoff, definition see findPeaks.centWave

xcmsSet.prefilter

prefilter=c(k,I), see findPeaks.centWave

xcmsSet.mzCenterFun

See findPeaks.centWave

xcmsSet.integrate

See findPeaks.centWave

xcmsSet.mzdiff

See findPeaks.centWave

xcmsSet.noise

See findPeaks.centWave

xcmsSet.verbose.columns

See findPeaks.centWave

xcmsSet.polarity

Filter raw data for positive/negative scans. See xcmsSet

xcmsSet.profparam

Parameters to use for profile generation. See xcmsSet

xcmsSet.nSlaves

The number of slaves/cores to be used for parallel peak detection. See xcmsSet

xcmsSet.fitgauss

See findPeaks.centWave

xcmsSet.sleep

The number of seconds to pause between plotting peak finding cycles. See findPeaks.centWave

xcmsSet.fwhm

See findPeaks.matchedFilter

xcmsSet.max

See findPeaks.matchedFilter

xcmsSet.step

See findPeaks.matchedFilter

group.bw0

See group.density

group.mzwid0

See group.density

group.bw

See group.density

group.mzwid

See group.density

group.minfrac

See group.density

group.minsamp

See group.density

group.max

See group.density

group.sleep

See group.density

retcor.method

See retcor

retcor.profStep

See retcor.obiwarp

retcor.plottype

See retcor.obiwarp

qcRlscSpan

The value of span for QC-RLSC

Author(s)

Bo Wen wenbo@genomics.cn


metaX documentation built on Oct. 5, 2016, 4:41 a.m.

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