{"id":868,"date":"2022-09-19T19:44:30","date_gmt":"2022-09-19T11:44:30","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=868"},"modified":"2022-09-19T19:44:30","modified_gmt":"2022-09-19T11:44:30","slug":"twilight%e5%a4%84%e7%90%86pangenome%e7%bb%93%e6%9e%9c","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=868","title":{"rendered":"twilight\u5904\u7406pangenome\u7ed3\u679c"},"content":{"rendered":"<p>github\u4e0b\u8f7d\u811a\u672c\uff08https:\/\/github.com\/ghoresh11\/twilight\uff09<br \/>\n\u9700\u8981\u7684R\u5305data.table\uff0cggplot2\uff0coptparse<\/p>\n<pre>Rscript classify_genes.R -p gene_presence_absence.Rtab -g groups.tab<\/pre>\n<p>\u5fc5\u987b\u53c2\u6570\uff1a<br \/>\n-p, &#8211;presence_absence\uff1aRoary \u6216 Panaroo\u8f93\u51fa\u7684gene_presence_absence.Rtab\u6587\u4ef6<br \/>\n-g, &#8211;grouping\uff1a\u4e00\u4e2a\u5236\u8868\u7b26\u5206\u9694\u7684\u5206\u7ec4\u6587\u4ef6<br \/>\n\u53ef\u9009\u53c2\u6570\uff1a<br \/>\n-o, &#8211;out\uff1a\u8f93\u51fa\u76ee\u5f55\u540d\u79f0\uff08\u9ed8\u8ba4=\u201cout\u201d\uff09\u3002<br \/>\n-m, &#8211;min_size\uff1a\u5ffd\u7565\u5c11\u4e8emin_size\u57fa\u56e0\u7ec4\u7684\u7ec4\uff08\u9ed8\u8ba4 = 10\uff09\u3002<br \/>\n-c, &#8211;core_threshold\uff1a\u7528\u4e8e\u5b9a\u4e49\u6bcf\u4e2a\u7ec4\u5185\u7684\u6838\u5fc3\u57fa\u56e0\u7684\u9608\u503c\uff08\u9ed8\u8ba4\u503c = 0.95\uff09\u3002<br \/>\n-r, &#8211;rare_threshold\uff1a\u7528\u4e8e\u5b9a\u4e49\u6bcf\u7ec4\u5185\u7a00\u6709\u57fa\u56e0\u7684\u9608\u503c\uff08\u9ed8\u8ba4\u503c = 0.15\uff09\u3002<br \/>\n-h, &#8211;help\uff1a\u6253\u5370\u5e2e\u52a9\u4fe1\u606f\u5e76\u9000\u51fa\u3002<br \/>\n\u8f93\u51fa\uff1a<br \/>\n1\u3001classification.tab \u57fa\u56e0\u7c07\u5728\u6bcf\u4e2a\u5206\u7c7b\u4e2d\u5b58\u5728\u7684\u5f62\u5f0f\uff08\u6838\u5fc3\u3001\u8f85\u52a9\u3001\u548c\u7a00\u6709\uff09<br \/>\n2\u3001frequencies.csv \u57fa\u56e0\u7c07\u5728\u6bcf\u4e2a\u5206\u79bb\u4e2d\u7684\u9891\u7387<br \/>\n3\u3001plots \u6587\u4ef6\u5939\uff0c\u5305\u542b\u67f1\u72b6\u56fe\u548cPCA\u56fe<\/p>\n","protected":false},"excerpt":{"rendered":"<p>github\u4e0b\u8f7d\u811a\u672c\uff08https:\/\/github.com\/ghoresh11\/twilight\uff09 \u9700\u8981\u7684R\u5305data.table\uff0cggplot2\uff0coptparse Rscript classify_genes.R -p gene_presence_absence.Rtab -g groups.tab \u5fc5\u987b\u53c2\u6570\uff1a -p, &#8211;presence_absence\uff1aRoary \u6216 Panaroo\u8f93\u51fa\u7684gene_presence_absence.Rtab\u6587\u4ef6 -g, &#8211;grouping\uff1a\u4e00\u4e2a\u5236\u8868\u7b26\u5206\u9694\u7684\u5206\u7ec4\u6587\u4ef6 \u53ef\u9009\u53c2\u6570\uff1a -o, &#8211;out\uff1a\u8f93\u51fa\u76ee\u5f55\u540d\u79f0\uff08\u9ed8\u8ba4=\u201cout\u201d\uff09\u3002 -m, &#8211;min_size\uff1a\u5ffd\u7565\u5c11\u4e8emin_size\u57fa\u56e0\u7ec4\u7684\u7ec4\uff08\u9ed8\u8ba4 = 10\uff09\u3002 -c, &#8211;core_threshold\uff1a\u7528\u4e8e\u5b9a\u4e49\u6bcf\u4e2a\u7ec4\u5185\u7684\u6838\u5fc3\u57fa\u56e0\u7684\u9608\u503c\uff08\u9ed8\u8ba4\u503c = 0.95\uff09\u3002 -r, &#8211;rare_threshold\uff1a\u7528\u4e8e\u5b9a\u4e49\u6bcf\u7ec4\u5185\u7a00\u6709\u57fa\u56e0\u7684\u9608\u503c\uff08\u9ed8\u8ba4\u503c = 0.15\uff09\u3002 -h, &#8211;help\uff1a\u6253\u5370\u5e2e\u52a9\u4fe1\u606f\u5e76\u9000\u51fa\u3002 \u8f93\u51fa\uff1a 1\u3001classification.tab \u57fa\u56e0\u7c07\u5728\u6bcf\u4e2a\u5206\u7c7b\u4e2d\u5b58\u5728\u7684\u5f62\u5f0f\uff08\u6838\u5fc3\u3001\u8f85\u52a9\u3001\u548c\u7a00\u6709\uff09 2\u3001frequencies.csv \u57fa\u56e0\u7c07\u5728\u6bcf\u4e2a\u5206\u79bb\u4e2d\u7684\u9891\u7387 3\u3001plots \u6587\u4ef6\u5939\uff0c\u5305\u542b\u67f1\u72b6\u56fe\u548cPCA\u56fe<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,10],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/868"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=868"}],"version-history":[{"count":1,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/868\/revisions"}],"predecessor-version":[{"id":869,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/868\/revisions\/869"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=868"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=868"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=868"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}