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| author | Alexander_Kabui | 2024-10-29 22:12:42 +0300 |
|---|---|---|
| committer | Alexander_Kabui | 2024-10-29 22:13:56 +0300 |
| commit | 4d2995d3ca8890bf49dd146510115a044dfb48c0 (patch) | |
| tree | 9ceb10ce46b1fc67e8b13d7fafc555000af378af /scripts | |
| parent | 4667ea4675f2ec3f545c5376a4f942ae2d9615d7 (diff) | |
| download | genenetwork3-4d2995d3ca8890bf49dd146510115a044dfb48c0.tar.gz | |
Refactor: pre compute kinship for both permutation and genome scan.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 20 |
1 files changed, 14 insertions, 6 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index f71fb08..ccbef84 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -221,11 +221,23 @@ print(Xcovar) # Function to perform scan1 + +cat("Computing the kinship") +if (method == "LMM"){ + kinship = calc_kinship(genome_prob) +} else if (method == "LOCO"){ + kinship = calc_kinship(genome_prob, "loco") +}else { + kinship = NULL +} + + perform_genome_scan <- function(cross, genome_prob, method="HK", addcovar = NULL, intcovar = NULL, + kinship = NULL, model = c("normal","binary"), Xcovar = NULL) { #' perform genome scan @@ -243,7 +255,6 @@ perform_genome_scan <- function(cross, if (method == "LMM") { # provide parameters for this cat("Performing scan1 using Linear mixed model\n") - kinship = calc_kinship(genome_prob) out <- scan1( genome_prob, cross$pheno, @@ -256,7 +267,6 @@ perform_genome_scan <- function(cross, ) } else if (method == "LOCO") { cat("Performing scan1 using Leave one chromosome out\n") - kinship = calc_kinship(genome_prob, "loco") out <- scan1( genome_prob, cross$pheno, @@ -288,6 +298,7 @@ perform_genome_scan <- function(cross, # Perform the genome scan for the cross object scan_results <- perform_genome_scan(cross = dataset, genome_prob = Pr, + kinship = kinship, method = SCAN_METHOD) scan_results @@ -345,6 +356,7 @@ perform_permutation_test <- function(cross, addcovar = NULL, intcovar = NULL, perm_Xsp = FALSE, + kinship = NULL, model = c("normal", "binary"), chr_lengths = NULL, perm_strata = NULL) { @@ -367,8 +379,6 @@ perform_permutation_test <- function(cross, cat("performing permutation test for the cross object\n") if (method == "HK") { - - perm <- scan1perm( genome_prob, cross$pheno, @@ -384,7 +394,6 @@ perform_permutation_test <- function(cross, ) } else if (method == "LMM") { - kinship = calc_kinship(genome_prob) perm <- scan1perm( genome_prob, cross$pheno, @@ -400,7 +409,6 @@ perform_permutation_test <- function(cross, ) } else if (method == "LOCO") { - kinship = calc_kinship(genome_prob, "loco") perm <- scan1perm( genome_prob, cross$pheno, |