diff --git a/R/run_carma.R b/R/run_carma.R index 3b8f714..ccee737 100644 --- a/R/run_carma.R +++ b/R/run_carma.R @@ -27,8 +27,10 @@ run_carma <- function(df, snp_col, z_col, effect_allele_col, bfile, threads = 1, sumstat <- df + plink_extract_ld_possibly <- purrr::possibly(levinmisc::plink_extract_ld) + ld <- df %>% - plink_extract_ld(bfile = bfile, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}}) + plink_extract_ld_possibly(bfile = bfile, plink_bin = plink_bin, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}}) if(is.null(ld)) { return(sumstat %>% mutate(ld_error = TRUE)) diff --git a/dev/flat_genomics_functions.Rmd b/dev/flat_genomics_functions.Rmd index eaf27da..48df51f 100644 --- a/dev/flat_genomics_functions.Rmd +++ b/dev/flat_genomics_functions.Rmd @@ -921,8 +921,10 @@ run_carma <- function(df, snp_col, z_col, effect_allele_col, bfile, threads = 1, sumstat <- df + plink_extract_ld_possibly <- purrr::possibly(levinmisc::plink_extract_ld) + ld <- df %>% - plink_extract_ld(bfile = bfile, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}}) + plink_extract_ld_possibly(bfile = bfile, plink_bin = plink_bin, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}}) if(is.null(ld)) { return(sumstat %>% mutate(ld_error = TRUE))