diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 31 |
1 files changed, 18 insertions, 13 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 4355769..1ff3e18 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -1,13 +1,12 @@ -# This script file contains the an implementation of qtl mapping using r-qtl2 -# For r-qtl1 implementation see: Scripts/rqtl_wrapper.R -# load the library +# This file contains an implementation of qtl mapping using r-qtl2 +# For r-qtl1 implementation see: ./rqtl_wrapper.R library(qtl2) library(rjson) - library(stringi) library(optparse) +# TODO add mapping function as a parameter: option_list <- list( make_option(c("-d", "--directory"), action = "store", default = NULL, type = "character", help="Temporary working directory: should also host the input file ."), @@ -61,6 +60,7 @@ genRandomFileName <- function(prefix, string_size = 9 , file_ext = ".txt") { # Step: Generate the control file name + control_file_path <- file.path(opt$directory, genRandomFileName(prefix = "control", file_ext = ".json")) cat("Generated the control file path at ", control_file_path, "\n") @@ -159,7 +159,6 @@ perform_genetic_pr <- function(cross, cores = NO_OF_CORES, step=1, map=NULL, - use_pseudomarkers=FALSE, map_function=c("haldane", "kosambi", "c-f", "morgan"), error_prob = 0.002 ) { @@ -173,19 +172,23 @@ perform_genetic_pr <- function(cross, #' @param step for default "1" #' @return a list of three-dimensional arrays of probabilities, individuals x genotypes x pst - - if (use_pseudomarkers){ - cat("Using pseudo markers for genetic probabilites\n") - map <- insert_pseudomarkers(cross$gmap, step=step) - } return(calc_genoprob(cross, map=map, error_prob=error_prob, map_function=map_function, quiet=FALSE, cores=cores)) } + +#Step: insert pseudomarkers to genetic map +# TODO need to review this to match rqtl1 +cat("Inserting pseudomarkers to the genetic map with steps", 1 , "and stepwidth" , "fixed\n") +MAP <- insert_pseudomarkers(cross$gmap, step= 1, stepwidth = "fixed", cores = NO_OF_CORES) + + # Step: calculate the genetic probabilities cat("Calculating the genetic probabilities\n") -Pr = perform_genetic_pr(cross) +Pr = perform_genetic_pr(cross, map = MAP) + + # Step: perform allele probabilites if cross ways @@ -207,14 +210,16 @@ error_lod <- do.call("cbind", error_lod) # TODO rework on this cat("Getting the phenotypes and covariates\n") pheno <- cross$pheno - covar <- match(cross$covar$sex, c("f", "m")) # make numeric +covar if (!is.null(covar)){ names(covar) <- rownames(cross$covar) + } print("The covariates are") -print(covar) +covar + Xcovar <- get_x_covar(cross) print("The Xcovar are ") print(Xcovar) |