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fix of the namespace reference error
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|---|---|---|
| @@ -1,65 +1,65 @@ | ||
| #Region "Microsoft.VisualBasic::dac12032440317c0959a8b4a01bff8de, Rscript\Library\mzkit_app\src\mzquant\mzDeco.vb" | ||
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| ' Author: | ||
| ' | ||
| ' xieguigang ([email protected], BioNovoGene Co., LTD.) | ||
| ' | ||
| ' Copyright (c) 2018 [email protected], BioNovoGene Co., LTD. | ||
| ' | ||
| ' | ||
| ' MIT License | ||
| ' | ||
| ' | ||
| ' Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| ' of this software and associated documentation files (the "Software"), to deal | ||
| ' in the Software without restriction, including without limitation the rights | ||
| ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| ' copies of the Software, and to permit persons to whom the Software is | ||
| ' furnished to do so, subject to the following conditions: | ||
| ' | ||
| ' The above copyright notice and this permission notice shall be included in all | ||
| ' copies or substantial portions of the Software. | ||
| ' | ||
| ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| ' SOFTWARE. | ||
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| ' /********************************************************************************/ | ||
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| ' Summaries: | ||
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| ' Code Statistics: | ||
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| ' Total Lines: 1359 | ||
| ' Code Lines: 896 (65.93%) | ||
| ' Comment Lines: 317 (23.33%) | ||
| ' - Xml Docs: 88.33% | ||
| ' | ||
| ' Blank Lines: 146 (10.74%) | ||
| ' File Size: 56.82 KB | ||
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| ' Module mzDeco | ||
| ' | ||
| ' Function: adjust_to_seconds, convertDataframeToXcmsPeaks, create_peakset, Deconv, dumpPeaks | ||
| ' expression, get_ionPeak, getIonPeak, ms1Scans, mz_deco | ||
| ' mz_groups, peakAlignment, peaksetMatrix, peaksSetMatrix, peakSubset | ||
| ' peaktable, pull_xic, read_rtshifts, readPeakData, readPeaktable | ||
| ' readSamples, readXcmsFeaturePeaks, readXcmsPeaks, readXcmsTableFile, readXIC | ||
| ' RI_batch_join, RI_calc, RI_reference, to_matrix, writePeaktable | ||
| ' writeSamples, writeXcmsPeaktable, writeXIC, writeXIC1, xcms_peak | ||
| ' xic_deco, xic_dtw_list, xic_matrix_list, XICpool_func | ||
| ' | ||
| ' Sub: Main | ||
| ' | ||
| ' /********************************************************************************/ | ||
| ' Author: | ||
| ' | ||
| ' xieguigang ([email protected], BioNovoGene Co., LTD.) | ||
| ' | ||
| ' Copyright (c) 2018 [email protected], BioNovoGene Co., LTD. | ||
| ' | ||
| ' | ||
| ' MIT License | ||
| ' | ||
| ' | ||
| ' Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| ' of this software and associated documentation files (the "Software"), to deal | ||
| ' in the Software without restriction, including without limitation the rights | ||
| ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| ' copies of the Software, and to permit persons to whom the Software is | ||
| ' furnished to do so, subject to the following conditions: | ||
| ' | ||
| ' The above copyright notice and this permission notice shall be included in all | ||
| ' copies or substantial portions of the Software. | ||
| ' | ||
| ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| ' SOFTWARE. | ||
|
|
||
|
|
||
|
|
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| ' /********************************************************************************/ | ||
|
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| ' Summaries: | ||
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|
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| ' Code Statistics: | ||
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| ' Total Lines: 1359 | ||
| ' Code Lines: 896 (65.93%) | ||
| ' Comment Lines: 317 (23.33%) | ||
| ' - Xml Docs: 88.33% | ||
| ' | ||
| ' Blank Lines: 146 (10.74%) | ||
| ' File Size: 56.82 KB | ||
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| ' Module mzDeco | ||
| ' | ||
| ' Function: adjust_to_seconds, convertDataframeToXcmsPeaks, create_peakset, Deconv, dumpPeaks | ||
| ' expression, get_ionPeak, getIonPeak, ms1Scans, mz_deco | ||
| ' mz_groups, peakAlignment, peaksetMatrix, peaksSetMatrix, peakSubset | ||
| ' peaktable, pull_xic, read_rtshifts, readPeakData, readPeaktable | ||
| ' readSamples, readXcmsFeaturePeaks, readXcmsPeaks, readXcmsTableFile, readXIC | ||
| ' RI_batch_join, RI_calc, RI_reference, to_matrix, writePeaktable | ||
| ' writeSamples, writeXcmsPeaktable, writeXIC, writeXIC1, xcms_peak | ||
| ' xic_deco, xic_dtw_list, xic_matrix_list, XICpool_func | ||
| ' | ||
| ' Sub: Main | ||
| ' | ||
| ' /********************************************************************************/ | ||
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| #End Region | ||
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@@ -70,6 +70,7 @@ Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache | |
| Imports BioNovoGene.Analytical.MassSpectrometry.Math | ||
| Imports BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram | ||
| Imports BioNovoGene.Analytical.MassSpectrometry.Math.Ms1 | ||
| Imports BioNovoGene.Analytical.MassSpectrometry.Math.Tasks | ||
| Imports BioNovoGene.Analytical.MassSpectrometry.SingleCells.Deconvolute | ||
| Imports Microsoft.VisualBasic.CommandLine.Reflection | ||
| Imports Microsoft.VisualBasic.ComponentModel.Collection | ||
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@@ -93,9 +94,9 @@ Imports SMRUCC.Rsharp.Runtime.Interop | |
| Imports SMRUCC.Rsharp.Runtime.Vectorization | ||
| Imports deco_math = BioNovoGene.Analytical.MassSpectrometry.Math.Extensions | ||
| Imports Matrix = SMRUCC.genomics.Analysis.HTS.DataFrame.Matrix | ||
| Imports RInternal = SMRUCC.Rsharp.Runtime.Internal | ||
| Imports std = System.Math | ||
| Imports vec = SMRUCC.Rsharp.Runtime.Internal.Object.vector | ||
| Imports RInternal = SMRUCC.Rsharp.Runtime.Internal | ||
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| ''' <summary> | ||
| ''' Extract peak and signal data from rawdata | ||
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