{"id":12466,"date":"2019-05-11T09:03:06","date_gmt":"2019-05-11T08:03:06","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/?p=12466"},"modified":"2019-05-11T09:05:02","modified_gmt":"2019-05-11T08:05:02","slug":"how-to-map-a-snp-or-cpg-site-to-the-proximal-gene-in-r","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2019\/05\/how-to-map-a-snp-or-cpg-site-to-the-proximal-gene-in-r\/","title":{"rendered":"How to map a SNP or CpG site to the proximal gene in R"},"content":{"rendered":"<p>There may be many ways, how to do that. Here are my favorite methods<\/p>\n<pre class=\"brush: php; title: ; notranslate\" title=\"\">\r\nSNP &lt;- c(&quot;rs123&quot;)\r\nBiocManager::install('grimbough\/biomaRt')\r\nlibrary(biomaRt)\r\nlibrary(plyr)\r\ngrch37.snp = useMart(biomart=&quot;ENSEMBL_MART_SNP&quot;, host=&quot;grch37.ensembl.org&quot;, path=&quot;\/biomart\/martservice&quot;,dataset=&quot;hsapiens_snp&quot;)\r\ngrch37 = useMart(biomart=&quot;ENSEMBL_MART_ENSEMBL&quot;, host=&quot;grch37.ensembl.org&quot;, path=&quot;\/biomart\/martservice&quot;, dataset=&quot;hsapiens_gene_ensembl&quot;)\r\nt1 &lt;- getBM(attributes = c(&quot;refsnp_id&quot;, &quot;ensembl_gene_stable_id&quot;, &quot;chr_name&quot;,&quot;chrom_start&quot;,&quot;chrom_end&quot;), filters = &quot;snp_filter&quot;, values = SNP, mart = grch37.snp)\r\nnames(t1)&#x5B;names(t1)==&quot;ensembl_gene_stable_id&quot;] &lt;- c(&quot;ensembl_gene_id&quot;)\r\nt2 &lt;- getBM(attributes = c(&quot;ensembl_gene_id&quot;,&quot;external_gene_name&quot;,&quot;start_position&quot;,&quot;end_position&quot;,&quot;description&quot;), filters = &quot;ensembl_gene_id&quot;, values =  ensembl_gene_id, mart = grch37)\r\njoin(t1,t2, type=&quot;left&quot;, by=&quot;ensembl_gene_id&quot;, match = &quot;first&quot;)\r\n<\/pre>\n<p>and<\/p>\n<pre class=\"brush: php; title: ; notranslate\" title=\"\">\r\nBiocManager::install('FDb.InfiniumMethylation.hg19')\r\nlibrary(FDb.InfiniumMethylation.hg19)\r\nCpG &lt;- c(&quot;cg00920043&quot;)\r\nhm450 &lt;- get450k()\r\nprobes &lt;- hm450&#x5B;CpG]\r\ngetNearestTSS(probes)\r\n<\/pre>\n\n<p>&nbsp;<\/p>\n<div class=\"bottom-note\">\n  <span class=\"mod1\">CC-BY-NC Science Surf , accessed 11.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"<p>There may be many ways, how to do that. Here are my favorite methods SNP &lt;- c(&quot;rs123&quot;) BiocManager::install(&#8216;grimbough\/biomaRt&#8217;) library(biomaRt) library(plyr) grch37.snp = useMart(biomart=&quot;ENSEMBL_MART_SNP&quot;, host=&quot;grch37.ensembl.org&quot;, path=&quot;\/biomart\/martservice&quot;,dataset=&quot;hsapiens_snp&quot;) grch37 = useMart(biomart=&quot;ENSEMBL_MART_ENSEMBL&quot;, host=&quot;grch37.ensembl.org&quot;, path=&quot;\/biomart\/martservice&quot;, dataset=&quot;hsapiens_gene_ensembl&quot;) t1 &lt;- getBM(attributes = c(&quot;refsnp_id&quot;, &quot;ensembl_gene_stable_id&quot;, &quot;chr_name&quot;,&quot;chrom_start&quot;,&quot;chrom_end&quot;), filters = &quot;snp_filter&quot;, values = SNP, mart = grch37.snp) names(t1)&#x5B;names(t1)==&quot;ensembl_gene_stable_id&quot;] &lt;- c(&quot;ensembl_gene_id&quot;) t2 &lt;- getBM(attributes = c(&quot;ensembl_gene_id&quot;,&quot;external_gene_name&quot;,&quot;start_position&quot;,&quot;end_position&quot;,&quot;description&quot;), &hellip; <a href=\"https:\/\/www.wjst.de\/blog\/sciencesurf\/2019\/05\/how-to-map-a-snp-or-cpg-site-to-the-proximal-gene-in-r\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">How to map a SNP or CpG site to the proximal gene in R<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[1363],"class_list":["post-12466","post","type-post","status-publish","format-standard","hentry","category-genetics-biology","tag-bioinformatics"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/12466","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=12466"}],"version-history":[{"count":3,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/12466\/revisions"}],"predecessor-version":[{"id":12469,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/12466\/revisions\/12469"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=12466"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=12466"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=12466"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}