diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 5 |
1 files changed, 3 insertions, 2 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 92cfd52..461b4a1 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -72,7 +72,6 @@ genRandomFileName <- function(prefix, string_size = 9, file_ext = ".txt") { # Generate control file path control_file_path <- file.path(opt$directory, genRandomFileName(prefix = "control", file_ext = ".json")) cat("Generated the control file path at", control_file_path, "\n") - # Read and parse the input file cat("Reading and parsing the input file.\n") json_data <- fromJSON(file = INPUT_FILE_PATH) @@ -181,7 +180,9 @@ error_lod <- do.call("cbind", error_lod) # Get phenotypes and covariates cat("Getting the phenotypes and covariates.\n") pheno <- cross$pheno -covar <- match(cross$covar$sex, c("f", "m")) # make numeric +# covar <- match(cross$covar$sex, c("f", "m")) # make numeric +# TODO rework on this +covar <- NULL if (!is.null(covar)) { names(covar) <- rownames(cross$covar) } |