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 +