run package msbuild

xieguigang · Dec 7, 2024 · 4070e64 · 4070e64
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diff --git a/Rscript/Library/mzkit_app/@export/xcms.d.ts b/Rscript/Library/mzkit_app/@export/xcms.d.ts
@@ -9,6 +9,23 @@
  * 
 */
 declare namespace xcms {
+   /**
+    * cast the xcms find peaks result raw dataframe to mzkit peak feature data
+    * 
+    * 
+     * @param x A dataframe result of the xcms ``findPeaks``. data could be generated via ``as.data.frame(findPeaks(data));``.
+     *  this raw data frame output contains data fields:
+     *  
+     *  1. mz, mzmin, mzmax
+     *  2. rt, rtmin, rtmax
+     *  3. into, intf
+     *  4. maxo, maxf
+     *  5. i
+     *  6. sn
+     * @param sample_name 
+     * + default value Is ``null``.
+   */
+   function cast_findpeaks_raw(x: object, sample_name?: string): object;
    /**
      * @param group_features default value Is ``false``.
      * @param env default value Is ``null``.

diff --git a/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms.md b/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms.md
@@ -3,3 +3,4 @@
 the xcms interop and data handler
 
 + [parse_xcms_samples](xcms/parse_xcms_samples.1) 
++ [cast_findpeaks_raw](xcms/cast_findpeaks_raw.1) cast the xcms find peaks result raw dataframe to mzkit peak feature data
diff --git a/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms/cast_findpeaks_raw.1 b/Rscript/Library/mzkit_app/man/mz_quantify/xcms/xcms/cast_findpeaks_raw.1
@@ -0,0 +1,31 @@
+.\" man page create by R# package system.
+.TH XCMS 1 2000-Jan "cast_findpeaks_raw" "cast_findpeaks_raw"
+.SH NAME
+cast_findpeaks_raw \- cast the xcms find peaks result raw dataframe to mzkit peak feature data
+.SH SYNOPSIS
+\fIcast_findpeaks_raw(\fBx\fR as <generic> dataframe, 
+\fBsample_name\fR as string = \fB<NULL>\fR);\fR
+.SH DESCRIPTION
+.PP
+cast the xcms find peaks result raw dataframe to mzkit peak feature data
+.PP
+.SH OPTIONS
+.PP
+\fBx\fB \fR\- 
+ A dataframe result of the xcms \fBfindPeaks\fR. data could be generated via \fBas.data.frame(findPeaks(data));\fR.
+ this raw data frame output contains data fields:
+
+ 1. mz, mzmin, mzmax
+ 2. rt, rtmin, rtmax
+ 3. into, intf
+ 4. maxo, maxf
+ 5. i
+ 6. sn
+. 
+.PP
+.SH SEE ALSO
+xcms
+.SH FILES
+.PP
+mz_quantify.dll
+.PP
diff --git a/.../mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XcmsSamplePeak.html b/.../mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XcmsSamplePeak.html
@@ -22,25 +22,38 @@ <h2>XcmsSamplePeak</h2>
 
         <h3>Description</h3>
 
-
+        <p>cast <code>findPeaks</code> result to dataframe</p>
 
         <h3>Declare</h3>        
 
         <pre>
             <code id="clr_ts">
 # namespace BioNovoGene.Analytical.MassSpectrometry.Math
 export class XcmsSamplePeak {
+   # 峰的索引或标识符。
    ID: string;
+   # 峰的峰下面积（峰的积分面积）。
    intb: double;
+   # 峰的总强度（积分强度）。
    into: double;
+   # 峰的最大过滤强度值。
+   maxf: double;
+   # 峰的最大原始强度值。
    maxo: double;
+   # 峰的中心质荷比（m/z）值。
    mz: double;
+   # 峰的最高质荷比（m/z）值。
    mzmax: double;
+   # 峰的最低质荷比（m/z）值。
    mzmin: double;
+   # 峰的中心保留时间（Retention Time，RT）。
    rt: double;
+   # 峰的结束保留时间。
    rtmax: double;
+   # 峰的起始保留时间。
    rtmin: double;
    sample: string;
+   # 峰的信噪比（Signal-to-Noise ratio）。
    sn: double;
 }
 </code>

diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms.html
@@ -86,6 +86,12 @@ <h1>xcms</h1>
     <a href="./xcms/parse_xcms_samples.html">parse_xcms_samples</a>
   </td>
   <td></td>
+</tr>
+<tr>
+  <td id="cast_findpeaks_raw">
+    <a href="./xcms/cast_findpeaks_raw.html">cast_findpeaks_raw</a>
+  </td>
+  <td><p>cast the xcms find peaks result raw dataframe to mzkit peak feature data</p></td>
 </tr></tbody>
       </table>
     </div>

diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/cast_findpeaks_raw.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/cast_findpeaks_raw.html
@@ -0,0 +1,79 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>cast the xcms find peaks result raw dataframe to mzkit peak feature data</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+    <link rel="stylesheet" type="text/css" href="https://mzkit.org/assets/js/page.css">
+</head>
+
+<body>
+    <div class="container">
+
+        <table style="width: 100%;">
+            <tr>
+                <td>cast_findpeaks_raw {xcms}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>cast the xcms find peaks result raw dataframe to mzkit peak feature data</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Usage</h3>
+
+        <div style="width: 100%; padding-left: 3%; color: black;">
+            <pre><code class='language-R' style="color: black; font-weight:normal;"><strong>cast_findpeaks_raw</strong>(<i>x</i>,
+    <i>sample.name</i> = <span style='color: blue !important;'>NULL</span>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>x</dt>
+<dd><p>A dataframe result of the xcms <code>findPeaks</code>. data could be generated via <code>as.data.frame(findPeaks(data));</code>.
+ this raw data frame output contains data fields:
+
+ 1. mz, mzmin, mzmax
+ 2. rt, rtmin, rtmax
+ 3. into, intf
+ 4. maxo, maxf
+ 5. i
+ 6. sn. [as <a href="/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/dataframe.html">dataframe</a>]</p></dd>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        BioNovoGene
+
+        <h3>Value</h3>
+
+        this function returns data object of type <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/PeakFeature.html">PeakFeature</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/PeakFeature.html">PeakFeature</a></li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>xcms</em> version 1.0.0.0 <a
+                href="../xcms.html">Index</a>]
+        </div>
+    </div>
+</body>
+
+<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
+<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
+<script type="text/javascript">r_highlights("example_r");</script>
+
+</html>
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,3 +3,4 @@
		the xcms interop and data handler

		+ [parse_xcms_samples](xcms/parse_xcms_samples.1)
		+ [cast_findpeaks_raw](xcms/cast_findpeaks_raw.1) cast the xcms find peaks result raw dataframe to mzkit peak feature data