{"id":2511,"date":"2019-12-28T23:12:48","date_gmt":"2019-12-28T22:12:48","guid":{"rendered":"https:\/\/myoceane.fr\/?p=2511"},"modified":"2020-01-25T09:49:24","modified_gmt":"2020-01-25T08:49:24","slug":"msnbase-%e8%b3%aa%e8%ad%9c%e5%84%80-r-%e6%8c%87%e4%bb%a4%e7%9a%84%e6%95%b4%e7%90%86","status":"publish","type":"post","link":"https:\/\/myoceane.fr\/index.php\/msnbase-%e8%b3%aa%e8%ad%9c%e5%84%80-r-%e6%8c%87%e4%bb%a4%e7%9a%84%e6%95%b4%e7%90%86\/","title":{"rendered":"[MSnbase] \u8cea\u8b5c\u5100 R, Python \u6307\u4ee4\u7684\u6574\u7406"},"content":{"rendered":"<div id=\"fb-root\"><\/div>\n\n<p style=\"text-align: justify;\">\u4e00\u822c\u5728\u7814\u7a76\u8cea\u8b5c\u5100\u7522\u751f\u51fa\u4f86\u7684\u8cc7\u8a0a\u6703\u4f7f\u7528 R \u7684 package\uff0c\u5f9e\u8cea\u8b5c\u5100\u51fa\u4f86\u7684\u8cc7\u6599\u683c\u5f0f\u4e3b\u8981\u662f RAW \u7684\u6a94\u6848\uff0c\u6839\u64da<a href=\"http:\/\/fields.scripps.edu\/rawconv\/\">\u9023\u7d50<\/a>\u7684\u4ecb\u7d39\uff0c\u4e00\u822c\u6703\u7d93\u904e\u4e00\u4e9b\u8f49\u6a94\u8b8a\u6210 MS1\/MS2, MGF \u6216\u8005\u662f mzXML. \u672c\u7bc7\u60f3\u8981\u7d00\u9304\u5728\u4f7f\u7528 library <a href=\"https:\/\/lgatto.github.io\/MSnbase\/articles\/v01-MSnbase-demo.html#sec:plotting\">MSnbase<\/a> \u7684\u6642\u5019\u4e00\u4e9b\u5be6\u7528\u7684\u6307\u4ee4\uff01<\/p>\n<h5>\u5229\u7528 R \u8b80\u53d6 Mgf \u6a94\u6848<\/h5>\n<pre class=\"lang:r\">mgf = readMgfData(\"\/home\/xxx\/R\/rawTest\/Alz_P11_H03_884_15Jul12_Roc_12-03-30.mgf\")\nmzID = mzID(\"\/home\/xxx\/R\/rawTest\/Alz_P11_H03_884_15Jul12_Roc_12-03-30_msgfplus.mzid\")<\/pre>\n\n\n\n<h5>\u5229\u7528\u00a0 Python \u8b80\u53d6 Mgf \u6a94\u6848<\/h5>\n<p>\u4ee5\u4e0b\u7684\u6307\u4ee4\u53c3\u8003<a href=\"https:\/\/pyteomics.readthedocs.io\/en\/latest\/data.html\">\u4f86\u6e90<\/a>\uff1a<\/p>\n<pre class=\"lang:python\">from pyteomics import mgf, auxiliary\nwith mgf.read('22Jan2016_Plasma_TBI_1.mgf') as reader:\n    auxiliary.print_tree(next(reader))<\/pre>\n<p>\u57f7\u884c\u4ee5\u4e0a\u7684\u7a0b\u5f0f\u4e4b\u5f8c\uff0c\u9996\u5148\u8f38\u51fa print_tree:<\/p>\n<pre class=\"lang:bash\">params\n -&gt; title\n -&gt; scans\n -&gt; rtinseconds\n -&gt; charge\n -&gt; pepmass\nm\/z array\nintensity array\ncharge array<\/pre>\n<p>\u6a94\u6848\u5206\u6210\u5e7e\u500b\u90e8\u5206\uff0cparams \u662f MGF \u6a94\u6848\u7684\u57fa\u672c\u8cc7\u6599\uff0c\u5728 python library \u63d0\u4f9b\u7684\u7bc4\u4f8b\u88e1\u9762\u53ef\u4ee5\u5305\u542b\u66f4\u591a\u7684\u8cc7\u8a0a\uff0c\u4f8b\u5982\u4ee5\u4e0b\uff1a<\/p>\n<pre><span class=\"go\">params<\/span>\n<span class=\"go\"> -&gt; username<\/span>\n<span class=\"go\"> -&gt; useremail<\/span>\n<span class=\"go\"> -&gt; mods<\/span>\n<span class=\"go\"> -&gt; pepmass<\/span>\n<span class=\"go\"> -&gt; title<\/span>\n<span class=\"go\"> -&gt; itol<\/span>\n<span class=\"go\"> -&gt; charge<\/span>\n<span class=\"go\"> -&gt; mass<\/span>\n<span class=\"go\"> -&gt; itolu<\/span>\n<span class=\"go\"> -&gt; it_mods<\/span>\n<span class=\"go\"> -&gt; com<\/span><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u822c\u5728\u7814\u7a76\u8cea\u8b5c\u5100\u7522\u751f\u51fa\u4f86\u7684\u8cc7\u8a0a\u6703\u4f7f\u7528 R \u7684 package\uff0c\u5f9e\u8cea\u8b5c\u5100\u51fa\u4f86\u7684\u8cc7\u6599\u683c\u5f0f\u4e3b\u8981\u662f RAW \u7684\u6a94\u6848\uff0c\u6839\u64da\u9023\u7d50\u7684\u4ecb\u7d39\uff0c\u4e00\u822c\u6703\u7d93\u904e\u4e00\u4e9b\u8f49\u6a94\u8b8a\u6210 MS1\/MS2, MGF \u6216\u8005\u662f mzXML. \u672c\u7bc7\u60f3\u8981\u7d00\u9304\u5728\u4f7f\u7528 library MSnbase \u7684\u6642\u5019\u4e00\u4e9b\u5be6\u7528\u7684\u6307\u4ee4\uff01<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[16,14],"tags":[],"class_list":["post-2511","post","type-post","status-publish","format-standard","hentry","category-health","category-it-technology"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - 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