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authorzsloan2021-07-23 19:40:04 +0000
committerzsloan2022-03-22 19:05:37 +0000
commit2849792ddc2e76750421c75d926d5a7f18c57e97 (patch)
treea3a36e9e77c45c366a57c2cc31e51f56ef9cfa1d
parente13e10d0f0dc96518e1d5efa9865ac2821b1c3f9 (diff)
downloadgenenetwork3-2849792ddc2e76750421c75d926d5a7f18c57e97.tar.gz
- Added scan_func function that determines whether scanone or scantwo
(pairscan) is used - For pairscan default to using step 20 (subject to change, but some step is required during calc.genoprob to make it run fast enough) - Added some new verbose prints
-rw-r--r--scripts/rqtl_wrapper.R40
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