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explodecomputer / tryx

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lexical error? #8

Closed yoonsucho closed 4 years ago

yoonsucho commented 4 years ago

x$candidate_instruments() Finding instruments for candidate traits Requesting default values. Extracting from pre-clumped data 78 out of 108 requested outcomes have pre-calculated instruments. Extracting data from 30 GWAS(s) and performing LD clumping [>] 1 of 30 Error: lexical error: invalid char in json text.

504 Gatewa (right here) ------^ In addition: Warning message: Error: lexical error: invalid char in json text. <html> <head><title>504 Gatewa (right here) ------^ </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/yoonsucho"><img src="https://avatars.githubusercontent.com/u/35306755?v=4" />yoonsucho</a> commented <strong> 4 years ago</strong> </div> <div class="markdown-body"> <p>The N for available GWAS is 600 with revised condition</p> <p>set_candidate_traits = function(id_list=NULL) { if(is.null(id_list)) { ao <- suppressMessages(TwoSampleMR::available_outcomes()) ids <- subset(ao, priority == 1 & nsnp > 10000000 & sample_size > 100000) %>% # have to go back to nsnp > 500000 & sample_size > 50000 important!!!!!!! arrange(desc(sample_size)) %>% filter(!duplicated(trait), mr == 1) %>% filter(!author %in% c("Shin", "Kettunen", "Roederer")) %>% filter(!grepl("ukb-b", id)) %>% filter(! id %in% c(dat$id.exposure[1], dat$id.outcome[1])) id_list <- ids$id message("Using default list of ", nrow(ids), " traits") } self$output$id_list <- id_list invisible(self$output$id_list) }</p> </div> </div> <div class="page-bar-simple"> </div> <div class="footer"> <ul class="body"> <li>© <script> document.write(new Date().getFullYear()) </script> Githubissues.</li> <li>Githubissues is a development platform for aggregating issues.</li> </ul> </div> <script src="https://cdn.jsdelivr.net/npm/jquery@3.5.1/dist/jquery.min.js"></script> <script src="/githubissues/assets/js.js"></script> <script src="/githubissues/assets/markdown.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/highlight.min.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/languages/go.min.js"></script> <script> hljs.highlightAll(); </script> </body> </html>