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yufree · Jan 2, 2020 · 79ef422 · 79ef422
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diff --git a/.travis.yml b/.travis.yml
diff --git a/05-rawdata.Rmd b/05-rawdata.Rmd
@@ -4,9 +4,9 @@ Raw data from the instruments such as LC-MS or GC-MS were hard to be analyzed. T
 
 - Indexed scan with time-stamp
 
-- Each scan contain a full scan mass spetrum with intensities
+- Each scan contains a full scan mass spectra
 
-Commen formats for open source mass spectrum data are mzxml, mzml or CDF. However, masscomp might shrink the data size[@yang2019].
+Commen formats for open source mass spectrum data are mzxml, mzml or CDF. However, **masscomp** might shrink the data size[@yang2019b].
 
 ## Peak extraction
 
@@ -24,7 +24,7 @@ time <- c(1:20)
 plot(intensity~time, type = 'o', main = 'EIC')
 ```
 
-However, in mass spectrumetry dataset, the EIC is not that simple for full scan. Due to the accuracy of instrument, the detected mass to charge ratio would have some shift and EIC would fail if different scan get the intensity from different mass to charge ratio. 
+However, due to the accuracy of instrument, the detected mass to charge ratio would have some shift and EIC would fail if different scan get the intensity from different mass to charge ratio. 
 
 In the `matchedfilter` algorithm[@smith2006], they solve this issue by bin the data in m/z dimension. The adjacent chromatographic slices could be combined to find a clean signal fitting fixed second-derivative Gaussian with full width at half-maximum
 (fwhm) of 30s to find peaks with about 1.5-4 times the signal peak width. The the integration is performed on the fitted area.
@@ -40,22 +40,25 @@ The `Centwave` algorithm[@tautenhahn2008] based on detection of regions of inter
 
 For single file, we could get peaks. However, we should make the peaks align across samples for subsquece analysis and retention time corrections should be performed. The basic idea behind retention time correction is that use the high quality grouped peaks to make a new retention time. You might choose `obiwarp`(for dramatic shifts) or loess regression(fast) method to get the corrected retention time for all of the samples. Remember the original retention times might be changed and you might need cross-correct the data. After the correction, you could group the peaks again for a better cross-sample peaks list. However, if you directly use `obiwarp`, you don't have to group peaks before correction.
 
-[@fu2017] show a matlab based shift correction methods
+[@fu2017] show a matlab based shift correction methods.
 
 ## Filling missing values
 
 Too many zeros or NA in peaks list are problematic for statistics. Then we usually need to integreate the area exsiting a peak. `xcms 3` could use profile matrix to fill the blank. They also have function to impute the NA data by replace missing values with a proportion of the row minimum or random numbers based on the row minimum. It depends on the user to select imputation methods as well as control the minimum fraction of featuers appeared in single group.
 
+```{r peakfilling, fig.show='hold', echo=FALSE,out.width= '90%', fig.cap='Peak filling of GC/LC-MS data',}
+knitr::include_graphics('images/peakfiling.png')
+```
+
 With many groups of samples, you will get another data matrix with column standing for peaks at cerntain retention time and row standing for samples after the Raw data pretreatment.
 
-```{r multidata, fig.show='hold', fig.cap='Demo of many GC/LC-MS data',echo=FALSE,,out.width='90%'}
+```{r multidata, fig.show='hold', fig.cap='Demo of many GC/LC-MS data',echo=FALSE,out.width='90%'}
 knitr::include_graphics('images/multidata.png')
 ```
 
 ## Spectral deconvolution
 
-Without fracmental infomation about certain compound, the peak extraction would suffer influnces from other compounds. At the same retention time, co-elute compounds might share similar mass. Hard electron ionization methods such as electron impact ionization (EI), APPI suffer this issue. So it would be hard to distighuish the co-elute peaks' origin and deconvolution method[
-@du2013] could be used to seperate different groups according to the similar chromatogragh beheviors. Another computational tool **eRah** could be a better solution for the whole process[@domingo-almenara2016]. Also the **ADAD-GC3.0** could also be helpful for such issue[@ni2016].
+Without fracmental infomation about certain compound, the peak extraction would suffer influnces from other compounds. At the same retention time, co-elute compounds might share similar mass. Hard electron ionization methods such as electron impact ionization (EI), APPI suffer this issue. So it would be hard to distighuish the co-elute peaks' origin and deconvolution method[@du2013] could be used to seperate different groups according to the similar chromatogragh beheviors. Another computational tool **eRah** could be a better solution for the whole process[@domingo-almenara2016]. Also the **ADAD-GC3.0** could also be helpful for such issue[@ni2016].
 
 ## Dynamic Range
 
@@ -78,6 +81,8 @@ tfit <- tobit(y ~ x, left = 0)
 summary(tfit)
 ```
 
+According to Ronald Hites's simulation[@hites2019], measurements below the LOD (even missing measurements) with the LOD/2 or with the $LOD/\sqrt2$ causes little bias and "Any time you have a % non-detected >20%, for whatever reason, it is unlikely that the data set can give useful results."
+
 ### Over Detection Limit
 
 **CorrectOverloadedPeaks** could be used to correct the Peaks Exceeding the Detection Limit issue[@lisec2016].
@@ -102,7 +107,7 @@ summary(tfit)
 
 - [OpenMS](http://www.openms.de/) is an open-source software C++ library for LC/MS data management and analyses[@rost2016]
 
-- [MZmatch](https://sourceforge.net/projects/mzmatch/) is a Java collection of small commandline tools specific for metabolomics MS data analysis [@scheltema2011a; @creek2012] 
+- [MZmatch](https://sourceforge.net/projects/mzmatch/) is a Java collection of small commandline tools specific for metabolomics MS data analysis [@scheltema2011; @creek2012] 
 
 - [iMet-Q](http://ms.iis.sinica.edu.tw/comics/Software_iMet-Q.html) is an automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data.[@chang2016]
 
@@ -151,7 +156,7 @@ xcmsSetdemoagain <- Reduce('c',list2)
 # for more higher order function in R, check here: http://www.johnmyleswhite.com/notebook/2010/09/23/higher-order-functions-in-r/
 ```
 
-- Use warpgroup to get peaks with better quality
+- Use **warpgroup** to get peaks with better quality
 
 ```{r eval=F}
 library(doParallel)

diff --git a/07-annotation.Rmd b/07-annotation.Rmd
@@ -222,7 +222,7 @@ This online [application](http://imet.seeslab.net/) is a network-based computati
 
 [MetExpert](https://sourceforge.net/projects/metexpert/) is an expert system to assist users with limited expertise in informatics to interpret GCMS data for metabolite identification without querying spectral databases[@qiu2018]
 
-## MS-DIA
+### MS-DIA
 
 - [decoMS2](https://pubs.acs.org/doi/10.1021/ac400751j) requires two different collision energies, low (usually 0V) and high, in each precursor range to solve the mathematical equations.[@nikolskiy2013]
 

diff --git a/_bookdown.yml b/_bookdown.yml
@@ -1,3 +1,4 @@
 book_filename: "Metabolomics"
 chapter_name: "Chapter "
 output_dir: docs
+delete_merged_file: true
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diff --git a/_bookdown_files/Metabolomics_files/figure-latex/Linear-1.pdf b/_bookdown_files/Metabolomics_files/figure-latex/Linear-1.pdf
diff --git a/_bookdown_files/Metabolomics_files/figure-latex/Linear-2.pdf b/_bookdown_files/Metabolomics_files/figure-latex/Linear-2.pdf
diff --git a/_bookdown_files/Metabolomics_files/figure-latex/demoeic-1.pdf b/_bookdown_files/Metabolomics_files/figure-latex/demoeic-1.pdf
diff --git a/_bookdown_files/Metabolomics_files/figure-latex/gtrends-1.pdf b/_bookdown_files/Metabolomics_files/figure-latex/gtrends-1.pdf
diff --git a/_bookdown_files/Metabolomics_files/figure-latex/quantile-1.pdf b/_bookdown_files/Metabolomics_files/figure-latex/quantile-1.pdf
diff --git a/_bookdown_files/Metabolomics_files/figure-latex/ratio-1.pdf b/_bookdown_files/Metabolomics_files/figure-latex/ratio-1.pdf
diff --git a/_bookdown_files/Metabolomics_files/figure-latex/ratio-2.pdf b/_bookdown_files/Metabolomics_files/figure-latex/ratio-2.pdf
diff --git a/_build.sh b/_build.sh
diff --git a/_deploy.sh b/_deploy.sh
diff --git a/_output.yml b/_output.yml
@@ -8,6 +8,7 @@ bookdown::gitbook:
         <li><a href="https://github.com/yufree/metaworkflow" target="blank">Published with bookdown</a></li>
     edit:
       link: https://github.com/yufree/metaworkflow/edit/master/%s
+    download: ["pdf","epub"]
 bookdown::pdf_book:
   includes:
     in_header: preamble.tex

diff --git a/book-output b/book-output
diff --git a/book.bib b/book.bib
@@ -4064,7 +4064,7 @@ @article{benavente2018
   journaltitle = {J. Sep. Sci.},
   date = {2018-07-03},
   pages = {1294-1304},
-  keywords = {UV,Plasma,MS,Neuropeptides,On-line,Preconcentration},
+  keywords = {MS,Neuropeptides,On-line,Plasma,Preconcentration,UV},
   author = {Benavente, Fernando and Medina-Casanellas, Silvia and Barbosa, Jos\'e and Sanz-Nebot, Victoria}
 }
 
@@ -7034,16 +7034,6 @@ @article{gao2019
   author = {Gao, Shixiong and Wan, Yi and Li, Wenjuan and Huang, Chong}
 }
 
-@article{yang2019,
-  langid = {english},
-  title = {{{MassComp}}, a Lossless Compressor for Mass Spectrometry Data},
-  doi = {10.1101/542894},
-  journaltitle = {bioRxiv},
-  date = {2019-02-06},
-  pages = {542894},
-  author = {Yang, Ruochen and Chen, Xi and Ochoa, Idoia}
-}
-
 @article{lindahl2016,
   title = {Overlap in Serum Metabolic Profiles between Non-Related Diseases: {{Implications}} for {{LC}}-{{MS}} Metabolomics Biomarker Discovery},
   volume = {478},
@@ -9838,4 +9828,32 @@ @article{jang2018
   author = {Jang, Cholsoon and Chen, Li and Rabinowitz, Joshua D.}
 }
 
+@article{yang2019b,
+  title = {{{MassComp}}, a Lossless Compressor for Mass Spectrometry Data},
+  volume = {20},
+  issn = {1471-2105},
+  doi = {10.1186/s12859-019-2962-7},
+  number = {1},
+  journaltitle = {BMC Bioinformatics},
+  date = {2019-07-01},
+  pages = {368},
+  author = {Yang, Ruochen and Chen, Xi and Ochoa, Idoia}
+}
+
+@article{nordstrom2006,
+  title = {Non-Linear {{Data Alignment}} for {{UPLC}}-{{MS}} and {{HPLC}}-{{MS}} Based {{Metabolomics}}: {{Application}} to {{Endogenous}} and {{Exogenous Metabolites}} in {{Human Serum}}},
+  volume = {78},
+  issn = {0003-2700},
+  doi = {10.1021/ac060245f},
+  shorttitle = {Non-Linear {{Data Alignment}} for {{UPLC}}-{{MS}} and {{HPLC}}-{{MS}} Based {{Metabolomics}}},
+  number = {10},
+  journaltitle = {Anal Chem},
+  date = {2006-05-15},
+  pages = {3289-3295},
+  author = {Nordstr\"om, Anders and O'Maille, Grace and Qin, Chuan and Siuzdak, Gary},
+  eprinttype = {pmid},
+  eprint = {16689529},
+  pmcid = {PMC3705959}
+}
+
 
diff --git a/docs/Metabolomics_files/figure-html/gtrends-1.png b/docs/Metabolomics_files/figure-html/gtrends-1.png
diff --git a/docs/annotation.html b/docs/annotation.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Miao YU" />
 
 
-<meta name="date" content="2019-12-20" />
+<meta name="date" content="2020-01-02" />
 
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   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -236,8 +236,8 @@
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+<li class="chapter" data-level="7.6.33" data-path="annotation.html"><a href="annotation.html#ms-dia"><i class="fa fa-check"></i><b>7.6.33</b> MS-DIA</a></li>
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 </ul></li>
 <li class="chapter" data-level="8" data-path="omics-analysis.html"><a href="omics-analysis.html"><i class="fa fa-check"></i><b>8</b> Omics analysis</a><ul>
 <li class="chapter" data-level="8.1" data-path="omics-analysis.html"><a href="omics-analysis.html#pathway-analysis"><i class="fa fa-check"></i><b>8.1</b> Pathway analysis</a><ul>
@@ -527,9 +527,8 @@ <h3><span class="header-section-number">7.6.31</span> magma</h3>
 <h3><span class="header-section-number">7.6.32</span> MetExpert</h3>
 <p><a href="https://sourceforge.net/projects/metexpert/">MetExpert</a> is an expert system to assist users with limited expertise in informatics to interpret GCMS data for metabolite identification without querying spectral databases<span class="citation">(Qiu, Lei, and Sumner <a href="#ref-qiu2018">2018</a>)</span></p>
 </div>
-</div>
-<div id="ms-dia" class="section level2">
-<h2><span class="header-section-number">7.7</span> MS-DIA</h2>
+<div id="ms-dia" class="section level3">
+<h3><span class="header-section-number">7.6.33</span> MS-DIA</h3>
 <ul>
 <li><p><a href="https://pubs.acs.org/doi/10.1021/ac400751j">decoMS2</a> requires two different collision energies, low (usually 0V) and high, in each precursor range to solve the mathematical equations.<span class="citation">(Nikolskiy et al. <a href="#ref-nikolskiy2013">2013</a>)</span></p></li>
 <li><p><a href="http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/">MS-DIAL</a> data independent MS/MS deconvolution for comprehensive metabolome analysis.<span class="citation">(Tsugawa et al. <a href="#ref-tsugawa2015">2015</a>)</span></p></li>
@@ -539,6 +538,7 @@ <h2><span class="header-section-number">7.7</span> MS-DIA</h2>
 <li><p><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.7b05318">SWATHtoMRM</a> Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery<span class="citation">(Zha et al. <a href="#ref-zha2018">2018</a>)</span></p></li>
 </ul>
 
+</div>
 </div>
 </div>
 <h3>References</h3>
@@ -688,7 +688,7 @@ <h3>References</h3>
 "link": null,
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-"download": null,
+"download": ["Metabolomics.pdf", "Metabolomics.epub"],
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diff --git a/docs/common-analysis-methods-for-metabolomics.html b/docs/common-analysis-methods-for-metabolomics.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Miao YU" />
 
 
-<meta name="date" content="2019-12-20" />
+<meta name="date" content="2020-01-02" />
 
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@@ -236,8 +236,8 @@
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 <li class="chapter" data-level="7.6.31" data-path="annotation.html"><a href="annotation.html#magma"><i class="fa fa-check"></i><b>7.6.31</b> magma</a></li>
 <li class="chapter" data-level="7.6.32" data-path="annotation.html"><a href="annotation.html#metexpert"><i class="fa fa-check"></i><b>7.6.32</b> MetExpert</a></li>
+<li class="chapter" data-level="7.6.33" data-path="annotation.html"><a href="annotation.html#ms-dia"><i class="fa fa-check"></i><b>7.6.33</b> MS-DIA</a></li>
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-<li class="chapter" data-level="7.7" data-path="annotation.html"><a href="annotation.html#ms-dia"><i class="fa fa-check"></i><b>7.7</b> MS-DIA</a></li>
 </ul></li>
 <li class="chapter" data-level="8" data-path="omics-analysis.html"><a href="omics-analysis.html"><i class="fa fa-check"></i><b>8</b> Omics analysis</a><ul>
 <li class="chapter" data-level="8.1" data-path="omics-analysis.html"><a href="omics-analysis.html#pathway-analysis"><i class="fa fa-check"></i><b>8.1</b> Pathway analysis</a><ul>
@@ -511,7 +511,7 @@ <h3>References</h3>
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diff --git a/docs/demo-1.html b/docs/demo-1.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Miao YU" />
 
 
-<meta name="date" content="2019-12-20" />
+<meta name="date" content="2020-01-02" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -236,8 +236,8 @@
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+<li class="chapter" data-level="7.6.33" data-path="annotation.html"><a href="annotation.html#ms-dia"><i class="fa fa-check"></i><b>7.6.33</b> MS-DIA</a></li>
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 <li class="chapter" data-level="8" data-path="omics-analysis.html"><a href="omics-analysis.html"><i class="fa fa-check"></i><b>8</b> Omics analysis</a><ul>
 <li class="chapter" data-level="8.1" data-path="omics-analysis.html"><a href="omics-analysis.html#pathway-analysis"><i class="fa fa-check"></i><b>8.1</b> Pathway analysis</a><ul>
@@ -632,7 +632,7 @@ <h2><span class="header-section-number">11.12</span> Summary</h2>
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diff --git a/docs/experimental-designdoe.html b/docs/experimental-designdoe.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Miao YU" />
 
 
-<meta name="date" content="2019-12-20" />
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   <meta name="viewport" content="width=device-width, initial-scale=1" />
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+<li class="chapter" data-level="7.6.33" data-path="annotation.html"><a href="annotation.html#ms-dia"><i class="fa fa-check"></i><b>7.6.33</b> MS-DIA</a></li>
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-<li class="chapter" data-level="7.7" data-path="annotation.html"><a href="annotation.html#ms-dia"><i class="fa fa-check"></i><b>7.7</b> MS-DIA</a></li>
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 <li class="chapter" data-level="8.1" data-path="omics-analysis.html"><a href="omics-analysis.html#pathway-analysis"><i class="fa fa-check"></i><b>8.1</b> Pathway analysis</a><ul>
@@ -447,7 +447,7 @@ <h3>References</h3>
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