diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 35 |
1 files changed, 32 insertions, 3 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 7bdc29a..c3f6932 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -196,6 +196,14 @@ print(Pr) summary(Pr) +# perform allele probabilites if cross ways + +# convert this to lower +if (dataset$crosstype == "4way"){ + # + aPr <- genoprob_to_alleleprob(pr) +} + #Function to Calculate genotyping error LOD scores cat("Calculate genotype error LOD scores\n") error_lod <- calc_errorlod(dataset, Pr, quiet = FALSE, cores = NO_OF_CORES) @@ -224,7 +232,10 @@ print(Xcovar) # Function to perform scan1 -cat("Computing the kinship") +# refactor this to a function + + +get_kinship <- function(probability, method="LMM"){ if (opt$method == "LMM"){ kinship = calc_kinship(genome_prob) } else if (opt$method == "LOCO"){ @@ -232,6 +243,16 @@ if (opt$method == "LMM"){ }else { kinship = NULL } +} + + +if (dataset$crosstype == "4way"){ + kinship <- get_kinship(aPr, opt$method) +} else { + kinship <- get_kinship(Pr, "loco") +} + + perform_genome_scan <- function(cross, @@ -285,7 +306,7 @@ perform_genome_scan <- function(cross, cat("Performing scan1 using Haley Knott\n") out <- scan1(genome_prob, cross$pheno, - addcovar = NULL, + addcovar = covar, intcovar = intcovar, model = model, Xcovar = Xcovar, @@ -298,10 +319,18 @@ perform_genome_scan <- function(cross, } # Perform the genome scan for the cross object -scan_results <- perform_genome_scan(cross = dataset, +if (dataset$crosstype == "4way"){ + sex <- (DOex$covar$Sex == "male")*1 + names(sex) <- rownames(dataset$covar) + sex <- setNames( (dataset$covar$Sex == "male")*1, rownames(DOex$covar)) + scan_results <- perform_genoeme_scan(aPr, dataset, kinship=kinship, method = "LOCO", addcovar = sex) +} else { + scan_results <- perform_genome_scan(cross = dataset, genome_prob = Pr, kinship = kinship, method = SCAN_METHOD) +} + scan_results |