diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl_wrapper.R | 51 |
1 files changed, 38 insertions, 13 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index 7518175..ffff5b9 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -11,6 +11,7 @@ option_list = list( make_option(c("-c", "--addcovar"), action="store_true", default=NULL, help="Use covariates (included as extra columns in the phenotype input file)"), make_option(c("--model"), type="character", default="normal", help="Mapping Model - Normal or Non-Parametric"), make_option(c("--method"), type="character", default="hk", help="Mapping Method - hk (Haley Knott), ehk (Extended Haley Knott), mr (Marker Regression), em (Expectation-Maximization), imp (Imputation)"), + make_option(c("--pairscan"), action="store_true", default=NULL, help="Run Pair Scan - the R/qtl function scantwo"), make_option(c("-i", "--interval"), action="store_true", default=NULL, help="Use interval mapping"), make_option(c("--nperm"), type="integer", default=0, help="Number of permutations"), make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata (stored as final column/vector in phenotype input file)"), @@ -155,6 +156,9 @@ cross_object = geno_to_csvr(geno_file, trait_names, trait_vals, cross_file) 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 for pair-scan\n') + cross_object <- calc.genoprob(cross_object, step=10) } else { verbose_print('Calculating genotype probabilities\n') cross_object <- calc.genoprob(cross_object) @@ -163,6 +167,7 @@ if (!is.null(opt$interval)) { # Pull covariates out of cross object, if they exist covars = vector(mode = "list", length = length(trait_names) - 1) if (!is.null(opt$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$pstrata)) { covar_names = trait_names[3:length(trait_names) - 1] @@ -175,16 +180,28 @@ if (!is.null(opt$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)){ @@ -195,19 +212,19 @@ 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$method) } } write.csv(perm_results, perm_out_file) @@ -220,10 +237,18 @@ if (!is.null(opt$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 scan\n') + qtl_results = scan_func(cross_object, pheno.col=1, model=opt$model, method=opt$method) +} + +verbose_print('Writing results to CSV file\n') +if (!is.null(opt$pairscan)) { + map_out_file = file.path(opt$outdir, paste("MAP_", opt$filename, sep = "" )) + write.csv(qtl_results[1], out_file) + write.csv(qtl_results[2], map_out_file) } else { - verbose_print('Running scanone\n') - qtl_results = scanone(cross_object, pheno.col=1, model=opt$model, method=opt$method) + write.csv(qtl_results, out_file) } -write.csv(qtl_results, out_file) |