diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 54 |
1 files changed, 13 insertions, 41 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index cbf2b93..78db11b 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -20,7 +20,7 @@ if (length(args) == 0) { json_file_path = args[1] } -# validation for the json file +# TODO validation for the json file if (!(file.exists(json_file_path))) { @@ -39,23 +39,9 @@ genRandomFileName <- function(prefix, file_ext = ".txt") { return(paste(randStr, file_ext, sep = "")) } -# this should be read from the json file assigned to variables -# 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 +# TODO work on the optional parameters # better fit for reading the data # make validations @@ -103,18 +89,9 @@ generate_cross_object <- function(json_data) { # alternatively pass a yaml file with -dataset <- write_control_file( - control_file_path, - crosstype = crosstype, - geno_file = geno_file, - pheno_file = pheno_file, - gmap_file = geno_map_file, - phenocovar_file = pheno_covar_file, - geno_codes = c(L = 1L, C = 2L), - alleles = alleles, - na.strings = c("-", "NA"), - overwrite = TRUE -) + + +generate_cross_object(json_data) # make validation for the data dataset <- read_cross2(control_file_path, quiet = FALSE) # replace this with a dynamic path @@ -177,7 +154,7 @@ error_lod <- calc_errorlod(dataset, Pr, quiet = FALSE, cores = 4) print(error_lod) -# Perform genome scane +# Perform genome scan # rework on this issue ## grab phenotypes and covariates; ensure that covariates have names attribute @@ -190,9 +167,8 @@ print(pheno) print(covar) print(Xcovar) -# rework on fetching th Xcovar and getting the covar data +# TODO: rework on fetching th Xcovar and getting the covar data -# perform kinship perform_genome_scan <- function(cross, @@ -292,7 +268,8 @@ perform_permutation_test <- function(cross, covar = NULL, Xcovar = NULL, perm_strata = NULL) { - # todo add chr_lengths and perm_Xsp + + # TODO! add chr_lengths and perm_Xsp if (method == "HKK") { perm <- scan1perm( @@ -332,7 +309,7 @@ perm <- perform_permutation_test(dataset, Pr, n_perm = 2, method = "LMM") # get the permutation summary with a significance threshold summary(perm, alpha = c(0.2, 0.05)) -# find function to perform the LOD peaks +# function to perform the LOD peaks find_lod_peaks <-function(scan_results, cross, threshold=4, drop=1.5){ # can this take pmap??? which map should we use??? @@ -340,13 +317,8 @@ find_lod_peaks <-function(scan_results, cross, threshold=4, drop=1.5){ print("Finding the lod peaks with thresholds n and drop n\n") return (find_peaks(scan_results, cross$gmap, threshold= threshold, drop=drop)) } - -# add the number of cores +# TODO! add the number of cores lod_peaks <- find_lod_peaks(results, dataset) -print(load_peaks) - -# how can we perform qtl effect computations ??? with input from user - -# what data should we return to the user +print(lod_peaks) -# improve on this script \ No newline at end of file +# TODO! format to return the data ??? \ No newline at end of file |