{"action":"created","issue":{"url":"https://api.github.com/repos/hakyimlab/PrediXcan/issues/12","labels_url":"https://api.github.com/repos/hakyimlab/PrediXcan/issues/12/labels{/name}","comments_url":"https://api.github.com/repos/hakyimlab/PrediXcan/issues/12/comments","events_url":"https://api.github.com/repos/hakyimlab/PrediXcan/issues/12/events","html_url":"https://github.com/hakyimlab/PrediXcan/pull/12","id":113742176,"number":12,"title":"Script for converting data from plink to dosage format now works correctly. ","user":{"login":"sritchie73","id":1674387,"avatar_url":"https://avatars.githubusercontent.com/u/1674387?v=3","gravatar_id":"","url":"https://api.github.com/users/sritchie73","html_url":"https://github.com/sritchie73","followers_url":"https://api.github.com/users/sritchie73/followers","following_url":"https://api.github.com/users/sritchie73/following{/other_user}","gists_url":"https://api.github.com/users/sritchie73/gists{/gist_id}","starred_url":"https://api.github.com/users/sritchie73/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sritchie73/subscriptions","organizations_url":"https://api.github.com/users/sritchie73/orgs","repos_url":"https://api.github.com/users/sritchie73/repos","events_url":"https://api.github.com/users/sritchie73/events{/privacy}","received_events_url":"https://api.github.com/users/sritchie73/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-10-28T04:42:46Z","updated_at":"2015-10-29T23:39:04Z","closed_at":"2015-10-29T21:20:32Z","pull_request":{"url":"https://api.github.com/repos/hakyimlab/PrediXcan/pulls/12","html_url":"https://github.com/hakyimlab/PrediXcan/pull/12","diff_url":"https://github.com/hakyimlab/PrediXcan/pull/12.diff","patch_url":"https://github.com/hakyimlab/PrediXcan/pull/12.patch"},"body":"Imputes missing data (SNPs with missing data for some, but not all samples) to 2 * the minor allele frequency of that SNP as per discussion in pull request #11 "},"comment":{"url":"https://api.github.com/repos/hakyimlab/PrediXcan/issues/comments/152357671","html_url":"https://github.com/hakyimlab/PrediXcan/pull/12#issuecomment-152357671","issue_url":"https://api.github.com/repos/hakyimlab/PrediXcan/issues/12","id":152357671,"user":{"login":"hakyim","id":2992313,"avatar_url":"https://avatars.githubusercontent.com/u/2992313?v=3","gravatar_id":"","url":"https://api.github.com/users/hakyim","html_url":"https://github.com/hakyim","followers_url":"https://api.github.com/users/hakyim/followers","following_url":"https://api.github.com/users/hakyim/following{/other_user}","gists_url":"https://api.github.com/users/hakyim/gists{/gist_id}","starred_url":"https://api.github.com/users/hakyim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hakyim/subscriptions","organizations_url":"https://api.github.com/users/hakyim/orgs","repos_url":"https://api.github.com/users/hakyim/repos","events_url":"https://api.github.com/users/hakyim/events{/privacy}","received_events_url":"https://api.github.com/users/hakyim/received_events","type":"User","site_admin":false},"created_at":"2015-10-29T23:39:04Z","updated_at":"2015-10-29T23:39:04Z","body":"Is this whole blood expression?\n\nOn Thursday, October 29, 2015, Scott Ritchie <notifications@github.com>\nwrote:\n\n> It looks like its performing pretty well now that the conversion from\n> plink to the dosage format imputes missing genotype data (and now that I\n> don't have the allele columns switched).\n>\n> plink uses different convention than we (and others) do in the sense that\n> the dosage refers to the number of the first allele. Do you mean that you\n> took this into account?\n>\n> Yes: in the first pull request I had the columns the wrong way around.\n> This has been fixed.\n>\n> Is the heritability of each gene available somewhere? It would be nice to\n> sanity check that the correlation between the predicted and actual\n> expression is high for genes with high heritability.\n>\n> We do find that R2 and h2 are in sync, see Figure 3 in the PrediXcan\n> paper. Red dots (R2) more or less follow black curve (h2). We'll make h2\n> available soon.\n>\n> Awesome. The R2 distribution I see is roughly the same shape as the h2\n> distribution in Figure 3.\n>\n> Also I see a small number of genes with strong negative correlation\n> between the predicted and actual gene expression. Is this something you've\n> seen before?\n>\n> Which expression data are you seeing this negative correlation?\n>\n> I see a negative correlation (< -0.1) for 134 genes in the DILGOM cohort:\n> a random sample (N = 518) of the working-age (24y – 75y) Finnish population\n> in Helsinki.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/hakyimlab/PrediXcan/pull/12#issuecomment-152354450>.\n>\n"}}