| sample | filename |
|---|---|
| ko15 | ko15.CDF |
| ko16 | ko16.CDF |
| wt15 | wt15.CDF |
| wt16 | wt16.CDF |
| timestamp*** | function | argument | value |
|---|---|---|---|
| Mon May 11 09:37:30 2020 | Peak detection | Object of class: CentWaveParam Parameters: ppm: 25 peakwidth: 20, 50 snthresh: 10 prefilter: 3, 100 mzCenterFun: wMean integrate: 1 mzdiff: -0.001 fitgauss: FALSE noise: 0 verboseColumns: FALSE roiList length: 0 firstBaselineCheck TRUE roiScales length: 0 | |
| Mon May 11 09:37:49 2020 | Peak grouping | Object of class: PeakDensityParam Parameters: sampleGroups: character of length 4 bw: 5 minFraction: 0.3 minSamples: 1 binSize: 0.01 maxFeatures: 50 | |
| Mon May 11 09:38:08 2020 | Retention time correction | Object of class: PeakGroupsParam Parameters: minFraction: 0.85 extraPeaks: 1 smooth: loess span: 0.2 family: gaussian subset: number of peak groups: 53 | |
| Mon May 11 09:38:09 2020 | Peak grouping | Object of class: PeakDensityParam Parameters: sampleGroups: character of length 4 bw: 20 minFraction: 0.4 minSamples: 1 binSize: 0.25 maxFeatures: 50 | |
| Mon May 11 09:38:18 2020 | Missing peak filling | Object of class: FillChromPeaksParam Parameters: expandMz: 0 expandRt: 0 ppm: 0 | |
MSn experiment data ("XCMSnExp")
Object size in memory: 1.55 Mb
- - - Spectra data - - -
MS level(s): 1
Number of spectra: 5112
MSn retention times: 41:38 - 75:7 minutes
- - - Processing information - - -
Data loaded [Mon May 11 09:37:30 2020]
MSnbase version: 2.10.1
- - - Meta data - - -
phenoData
rowNames: 1 2 3 4
varLabels: sample_name sample_group
varMetadata: labelDescription
Loaded from:
[1] ko15.CDF... [4] wt16.CDF
Use 'fileNames(.)' to see all files.
protocolData: none
featureData
featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
fvarLabels: fileIdx spIdx ... spectrum (31 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
method: centWave
15405 peaks identified in 4 samples.
On average 3851 chromatographic peaks per sample.
Alignment/retention time adjustment:
method: peak groups
Correspondence:
method: chromatographic peak density
6349 features identified.
Median mz range of features: 0
Median rt range of features: 0
6154 filled peaks (on average 1538.5 per sample).
An "xcmsSet" object with 4 samples
Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes)
Mass range: 200.1-600 m/z
Peaks: 15405 (about 3851 per sample)
Peak Groups: 6349
Sample classes: KO, WT
Feature detection:
o Peak picking performed on MS1.
o Scan range limited to 1 - 1278
Profile settings: method = bin
step = 0.1
Memory usage: 3.98 MB