diff options
| -rw-r--r-- | scripts/rqtl_wrapper.R | 40 |
1 files changed, 28 insertions, 12 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index 4c96ff2..0d13ccb 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -175,6 +175,9 @@ cross_object = geno_to_csvr(geno_file, trait_names, trait_vals, cross_file, type if (!is.null(opt$interval)) { verbose_print('Calculating genotype probabilities with interval mapping\n') cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max") +} else if (!is.null(opt$pairscan)) { + verbose_print('Calculating genotype probabilities with interval mapping\n') + cross_object <- calc.genoprob(cross_object, step=20) } else { verbose_print('Calculating genotype probabilities\n') cross_object <- calc.genoprob(cross_object) @@ -189,6 +192,7 @@ if (type == "4-way") { # Pull covariates out of cross object, if they exist covars <- c() # Holds the covariates which should be passed to R/qtl if (!is.null(opt$addcovar)) { + verbose_print('Pulling covariates out of cross object\n') # If perm strata are being used, it'll be included as the final column in the phenotype file if (!is.null(opt$pstrata)) { covar_names = trait_names[2:(length(trait_names)-1)] @@ -224,16 +228,28 @@ if (!is.null(opt$addcovar)) { # Pull permutation strata out of cross object, if it is being used perm_strata = vector() if (!is.null(opt$pstrata)) { + verbose_print('Pulling permutation strata out of cross object\n') strata_col = trait_names[length(trait_names)] perm_strata <- pull.pheno(cross_object, strata_col) } # If a marker name is supplied as covariate, get its vector of values and add them as a covariate if (!is.null(opt$control)) { + verbose_print('Creating marker covariates and binding them to covariates vector\n') marker_covars = create_marker_covars(cross_object, opt$control) covars <- cbind(covars, marker_covars) } +if (!is.null(opt$pairscan)) { + scan_func <- function(...){ + scantwo(...) + } +} else { + scan_func <- function(...){ + scanone(...) + } +} + # Calculate permutations if (opt$nperm > 0) { if (!is.null(opt$filename)){ @@ -244,19 +260,19 @@ if (opt$nperm > 0) { if (!is.null(opt$addcovar) || !is.null(opt$control)){ if (!is.null(opt$pstrata)) { - verbose_print('Running ', opt$nperm, ' permutations with cofactors and strata\n') - perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method) + verbose_print('Running permutations with cofactors and strata\n') + perm_results = scan_func(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method) } else { - verbose_print('Running ', opt$nperm, ' permutations with cofactors\n') - perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, model=opt$model, method=opt$method) + verbose_print('Running permutations with cofactors\n') + perm_results = scan_func(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, model=opt$model, method=opt$method) } } else { if (!is.null(opt$pstrata)) { - verbose_print('Running ', opt$nperm, ' permutations with strata\n') - perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method) + verbose_print('Running permutations with strata\n') + perm_results = scan_func(cross_object, pheno.col=1, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method) } else { - verbose_print('Running ', opt$nperm, ' permutations\n') - perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, model=opt$model, method=opt$method) + verbose_print('Running permutations\n') + perm_results = scan_func(cross_object, pheno.col=1, n.perm=opt$nperm, model=opt$model, method=opt$method) } } write.csv(perm_results, perm_out_file) @@ -269,11 +285,11 @@ if (!is.null(opt$filename)){ } if (!is.null(opt$addcovar) || !is.null(opt$control)){ - verbose_print('Running scanone with cofactors\n') - qtl_results = scanone(cross_object, pheno.col=1, addcovar=covars, model=opt$model, method=opt$method) + verbose_print('Running scan with cofactors\n') + qtl_results = scan_func(cross_object, pheno.col=1, addcovar=covars, model=opt$model, method=opt$method) } else { - verbose_print('Running scanone\n') - qtl_results = scanone(cross_object, pheno.col=1, model=opt$model, method=opt$method) + verbose_print('Running scan\n') + qtl_results = scan_func(cross_object, pheno.col=1, model=opt$model, method=opt$method) } #QTL main effects on adjusted longevity |