From 4ac23b7be8e17bc6c7a0f7026fa41d7052fc9be6 Mon Sep 17 00:00:00 2001 From: Gibran Hemani Date: Fri, 29 Nov 2024 08:30:10 +0000 Subject: [PATCH] added bmiz and pp prs weights --- resources/genotypes/tophits/bmiz.txt | 458 +++++++++++++++++++++++++++ resources/genotypes/tophits/pp.txt | 282 +++++++++++++++++ test/tophits.r | 12 +- 3 files changed, 749 insertions(+), 3 deletions(-) create mode 100644 resources/genotypes/tophits/bmiz.txt create mode 100644 resources/genotypes/tophits/pp.txt diff --git a/resources/genotypes/tophits/bmiz.txt b/resources/genotypes/tophits/bmiz.txt new file mode 100644 index 0000000..3c27726 --- /dev/null +++ b/resources/genotypes/tophits/bmiz.txt @@ -0,0 +1,458 @@ +1:32196647_C_G C -0.0160597 +1:62579891_G_T G 0.033075 +1:98315893_A_G A -0.0157008 +1:110082551_G_T G 0.0684263 +1:111338672_A_G A -0.0256435 +1:112324111_A_T A -0.0143963 +1:156489974_A_G A 0.0140775 +1:174321997_A_G A 0.0224585 +1:11207269_C_T C 0.0133837 +1:16848652_A_G A 0.0111552 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bind_rows(traits, tibble(Name = "Pulse pressure", "pheno_id" = "pp", "opengwasid" = "ebi-a-GCST90018970")) +i <- 23 +lapply(1:nrow(traits), \(i) { of <- here("resources", "genotypes", "tophits", paste0(traits$pheno_id[i], ".txt")) if(traits$pheno_id[i] == "depression") { return(NULL) @@ -23,7 +24,7 @@ lapply(13:nrow(traits), \(i) { if(!file.exists(of)) { message(i, " " , of) a <- try(tophits(traits$opengwasid[i])) - if(class(a) != "try-error") + if(! "try-error" %in% class(a)) { if(nrow(a) > 0) { a <- a %>% @@ -31,8 +32,13 @@ lapply(13:nrow(traits), \(i) { select(vid, ea, beta) write.table(a, file=of, row=F, col=F, qu=F) } + if(traits$pheno_id[i] == "bmi") { + of <- here("resources", "genotypes", "tophits", paste0("bmiz.txt")) + write.table(a, file=of, row=F, col=F, qu=F) + } } } }) +