Open privefl opened 1 month ago
library(bigsnpr) bigsnp <- snp_attachExtdata() G <- bigsnp$genotypes corr0 <- snp_cor(G) corr <- as_SFBM(corr0) gwas <- big_univLinReg(G, rnorm(nrow(G))) df_beta <- dplyr::transmute(gwas, beta = estim, beta_se = std.err, n_eff = nrow(G)) snp_ldpred2_auto(corr, df_beta, 0.01) G[, 1] <- 0 corr0.2 <- snp_cor(G) corr.2 <- as_SFBM(corr0.2) # Here should start to error, instead of returning some BS snp_ldpred2_auto(corr.2, df_beta, 0.01) snp_ldpred2_grid(corr.2, df_beta, data.frame(h2 = 0.01, p = 0.1, sparse = FALSE)) # snp_ldpred2_inf(corr.2, df_beta, h2 = 0.01) # run indefinitely snp_lassosum2(corr.2, df_beta, delta = 0.01)