diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 87 |
1 files changed, 84 insertions, 3 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 78db11b..db4797a 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -70,7 +70,78 @@ str_glue("Generated control file path is {control_file_path}") # think about the issue about geno codes ~~~~ # function to generate a cross file from a json list + + +# work on the default from the json_data validation here +# better defaults for the json file + + +json_data + +json_data$na_strings + + +if (is.null(json_data$sep)){ +cat("Using ',' as a default sep for cross file\n") +json_data$sep = "," +} + +if (is.null(json_data$na.strings)){ +cat("Using '-' and 'NA' as the default na.strings\n") + json_data$na.strings = c("-" , "NA") +} + +if (is.null(json_data$geno_transposed)) { +cat("Using FALSE as default parameter for geno_transposed\n") +json_data$geno_transposed = FALSE +} + +if (is.null(json_data$founder_geno_transposed)){ +cat("Using FALSE as default parameter for founder_geno_transposed\n") +json_data$founder_geno_transposed = FALSE +} + + +if (is.null(json_data$pheno_transposed)) { +cat("Using FALSE as default parameter for pheno_transposed\n") +json_data$geno_transposed = FALSE +} + + + +if( is.null(json_data$covar_transposed) ){ +cat("Using FALSE as default parameter for covar_transposed\n") +json_data$covar_transposed = FALSE +} + + +if (is.null(json_data$phenocovar_transposed)){ +cat("Using FALSE as default parameter for phenocovar_transposed\n") +json_data$phenocovar_transposed = FALSE +} + + + +# probably check on using a dict for check this parameter +# more like default object parameter + + +cross_default1 <- c( + "sep" = ",", + "na_strings" = c("-", "NA"), + "geno_transposed" = FALSE, + "covar_transposed" = FALSE, + "pheno_transposed" = FALSE, + "founder_geno_transposed" = FALSE, + "phenocovar_transposed" = FALSE + +) + + + +# mssing something here generate_cross_object <- function(json_data) { + # function to write the cross object from a json data object return ( write_control_file( control_file_path, @@ -78,10 +149,21 @@ generate_cross_object <- function(json_data) { geno_file = json_data$geno_file, pheno_file = json_data$pheno_file, gmap_file = json_data$geno_map_file, + pmap_file = json_data$pheno_map_file, phenocovar_file = json_data$phenocovar_file, geno_codes = json_data$geno_codes, alleles = json_data$alleles, na.strings = json_data$na.strings, + geno_transposed = json_data$geno_transposed, + sex_file = json_data$sex_file, + founder_geno_file = json_data$founder_geno_file, + covar_file = json_data$covar_file, + sex_covar = json_data$sex_covar, + sex_codes = json_data$sex_codes, + crossinfo_file = json_data$crossinfo_file, + crossinfo_covar = json_data$crossinfo_covar, + crossinfo_codes = json_data$crossinfo_codes, + xchr = json_data$xchr, overwrite = TRUE ) ) @@ -90,13 +172,12 @@ generate_cross_object <- function(json_data) { # alternatively pass a yaml file with - generate_cross_object(json_data) -# make validation for the data dataset <- read_cross2(control_file_path, quiet = FALSE) # replace this with a dynamic path - # check integrity of the cross + + cat("Check the integrity of the cross object") check_cross2(dataset) if (check_cross2(dataset)) { |