diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 74 |
1 files changed, 68 insertions, 6 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 30806b8..9d41c6a 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -18,11 +18,11 @@ if (length(args)==0) { } else { json_file_path = args[1] - # convert this to an absolute file path - } -# validation for the json file +# validation for the json file + + if (!(file.exists(json_file_path))) { stop("The input file path does not exists") } else { @@ -31,11 +31,10 @@ json_data = fromJSON(file = json_file_path) } + # generate random string file path here genRandomFileName <- function(prefix,file_ext=".txt"){ - randStr = paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_") - return(paste(randStr,file_ext,sep="")) } @@ -43,12 +42,25 @@ genRandomFileName <- function(prefix,file_ext=".txt"){ # TODO improve on this or use option + +# should put constraints for items data required for this crosstype <- json_data$crosstype geno_file <- json_data$geno_file pheno_file <- json_data$pheno_file geno_map_file <- json_data$geno_map_file pheno_covar_file <- json_data$phenocovar_file alleles <- json_data$alleles +founder_geno_file = json_data$founder_geno_file +gmap_file = json_data$gmap_file + + +# work on the optional parameters + +# better fit for reading the data +# make validations + +# parsing the required data for example the geno_codes + # geno_codes handle the geno codes here @@ -69,6 +81,24 @@ str_glue( # issue I can no define the different paths for files for example pheno_file +# think about the issue about geno codes ~~~~ +# function to generate a cross file from a json list + +generate_cross_object <- function(json_data){ +return (write_control_file(control_file_path, + crosstype= json_data$crosstype, + geno_file= json_data$geno_file, + pheno_file= json_data$pheno_file, + gmap_file= json_data$geno_map_file, + phenocovar_file= json_data$phenocovar_file, + geno_codes= json_data$geno_codes, + alleles= json_data$alleles, + na.strings=json_data$na.strings, + overwrite = TRUE)) +} + + +# alternatively pass a yaml file with dataset <- write_control_file(control_file_path, crosstype= crosstype, geno_file= geno_file, @@ -80,7 +110,6 @@ dataset <- write_control_file(control_file_path, na.strings=c("-", "NA"), overwrite = TRUE) - # make validation for the data dataset <- read_cross2(control_file_path, quiet = FALSE) # replace this with a dynamic path @@ -108,3 +137,36 @@ cat(" IDs for all individuals in the dataset object that have phenotype data") ind_ids_pheno(dataset) cat("Name of the founder Strains/n") founders(dataset) + +# Work on computing the genetic probabilities + + +analysis_type <- "single" + + +perform_genetic_pr <- function(cross, cores= 1, error_prob=0.002, analysis_type="single"){ +# improve on this +if (analysis_type == "single"){ + pr <- calc_genoprob(cross, error_prob= error_prob, quiet=FALSE, cores=cores) + return (pr) +} +} + +# get the genetic probability + +Pr = perform_genetic_pr(dataset) +cat("Summaries on the genetic probabilites \n") +print(Pr) +summary(Pr) + + +#calculate genotyping error LOD scores, to help identify potential genotyping errors (and problem markers and/or individuals +error_lod <- calc_errorlod(dataset, Pr, quiet = FALSE, cores = 4) +print(error_lod) + + +# + + + + |