diff --git a/R/MRlap.R b/R/MRlap.R index fa14905..66ebefa 100644 --- a/R/MRlap.R +++ b/R/MRlap.R @@ -117,6 +117,8 @@ MRlap <- function(exposure, hm3 = normalizePath(hm3) } else stop("hm3 : wrong format, should be character", call. = FALSE) + ## default is to need the CHR:POS info. Only exception is if using local Plink clumping + need_chrpos=TRUE ## user-provided SNP list? if (!do_pruning){ @@ -145,7 +147,6 @@ MRlap <- function(exposure, if(MR_pruning_LD<0) stop("MR_pruning_LD : should be positive", call. = FALSE) if(MR_pruning_LD>1) stop("MR_pruning_LD : should not be larger than 1", call. = FALSE) - need_chrpos=TRUE if(MR_pruning_LD>0){ if(verbose) cat("The LD threshold used for pruning MR instruments is:", MR_pruning_LD, "\n") if(!is.null(MR_plink)){