{"action":"created","issue":{"url":"https://api.github.com/repos/privefl/bigsnpr/issues/15","repository_url":"https://api.github.com/repos/privefl/bigsnpr","labels_url":"https://api.github.com/repos/privefl/bigsnpr/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/privefl/bigsnpr/issues/15/comments","events_url":"https://api.github.com/repos/privefl/bigsnpr/issues/15/events","html_url":"https://github.com/privefl/bigsnpr/issues/15","id":367410521,"node_id":"MDU6SXNzdWUzNjc0MTA1MjE=","number":15,"title":"Further pruning using snp_autoSVD( ) on previously pruned data","user":{"login":"bweedop","id":22863168,"node_id":"MDQ6VXNlcjIyODYzMTY4","avatar_url":"https://avatars3.githubusercontent.com/u/22863168?v=4","gravatar_id":"","url":"https://api.github.com/users/bweedop","html_url":"https://github.com/bweedop","followers_url":"https://api.github.com/users/bweedop/followers","following_url":"https://api.github.com/users/bweedop/following{/other_user}","gists_url":"https://api.github.com/users/bweedop/gists{/gist_id}","starred_url":"https://api.github.com/users/bweedop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bweedop/subscriptions","organizations_url":"https://api.github.com/users/bweedop/orgs","repos_url":"https://api.github.com/users/bweedop/repos","events_url":"https://api.github.com/users/bweedop/events{/privacy}","received_events_url":"https://api.github.com/users/bweedop/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-10-06T01:19:00Z","updated_at":"2018-10-25T23:45:44Z","closed_at":null,"author_association":"NONE","body":"I am running the snp_autoSVD function on a set of SNPs and then once again on a subsequent subset of SNPs afterward. After the pruning and removal of long-range LD regions, I ran the same function on randomly selected subsets (10K SNPs and 50K SNPs) of the already pruned set of SNPs and both are pruned even further, reduced down to a set of ~6K SNPs and ~28K SNPs. \r\n\r\nI am wondering what is happening and I am hoping that you could shed some light on if snp_autoSVD() might come into play here. Why would a subset of the pruned SNPs be pruned even further?"},"comment":{"url":"https://api.github.com/repos/privefl/bigsnpr/issues/comments/433241490","html_url":"https://github.com/privefl/bigsnpr/issues/15#issuecomment-433241490","issue_url":"https://api.github.com/repos/privefl/bigsnpr/issues/15","id":433241490,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMzI0MTQ5MA==","user":{"login":"bweedop","id":22863168,"node_id":"MDQ6VXNlcjIyODYzMTY4","avatar_url":"https://avatars3.githubusercontent.com/u/22863168?v=4","gravatar_id":"","url":"https://api.github.com/users/bweedop","html_url":"https://github.com/bweedop","followers_url":"https://api.github.com/users/bweedop/followers","following_url":"https://api.github.com/users/bweedop/following{/other_user}","gists_url":"https://api.github.com/users/bweedop/gists{/gist_id}","starred_url":"https://api.github.com/users/bweedop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bweedop/subscriptions","organizations_url":"https://api.github.com/users/bweedop/orgs","repos_url":"https://api.github.com/users/bweedop/repos","events_url":"https://api.github.com/users/bweedop/events{/privacy}","received_events_url":"https://api.github.com/users/bweedop/received_events","type":"User","site_admin":false},"created_at":"2018-10-25T23:45:44Z","updated_at":"2018-10-25T23:45:44Z","author_association":"NONE","body":"Hey Florian. In order to still use snp_autoSVD, I cloned your package and altered the arguments in the function to include the option of using the physical distance window rather than the number of adjacent SNPS. You can take a look at what I changed here; Can think of any issues this would cause? Also, while this is a minor change, I can push this change if you'd like to add this functionality.\r\n\r\n` snp_autoSVD <- function(G,\r\n                        infos.chr,\r\n                        infos.pos,\r\n                        ind.row = rows_along(G),\r\n                        ind.col = cols_along(G),\r\n                        fun.scaling = snp_scaleBinom(),\r\n                        thr.r2 = 0.2,\r\n                        size = 500,\r\n                        k = 10,\r\n                        roll.size = 50,\r\n                        int.min.size = 20,\r\n                        is.size.in.bp = FALSE\r\n                        ncores = 1,\r\n                        verbose = TRUE) {\r\n\r\n  check_args()\r\n\r\n  # Verbose?\r\n  printf2 <- function(...) if (verbose) printf(...)\r\n\r\n  # First clumping\r\n  THR <- thr.r2\r\n  printf2(\"Phase of clumping at r2 > %s.. \", THR)\r\n  ind.keep <- snp_clumping(G, \r\n                           infos.chr = infos.chr, \r\n                           ind.row = ind.row,\r\n                           exclude = setdiff(cols_along(G), ind.col),\r\n                           thr.r2 = THR,\r\n                           size = size,\r\n                           is.size.in.bp = is.size.in.bp,\r\n                           infos.pos = infos.pos,\r\n                           ncores = ncores) `\r\n"}}
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