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| author | zsloan | 2021-01-06 11:51:01 -0600 |
|---|---|---|
| committer | zsloan | 2021-01-06 11:51:01 -0600 |
| commit | 7bcc5d1e8111d7c74299c7f017c4a0427f8b4830 (patch) | |
| tree | 63ff05a15e1e5ac14f650c29e1d10d73725c8a4e | |
| parent | 834a8c167df3c4d08c144fc614402347256e9af7 (diff) | |
| download | genenetwork2-7bcc5d1e8111d7c74299c7f017c4a0427f8b4830.tar.gz | |
Changes to the way R/qtl deals with 4-way crosses so it will work with new HET3-ITP genotypes
| -rw-r--r-- | wqflask/wqflask/marker_regression/rqtl_mapping.py | 10 |
1 files changed, 2 insertions, 8 deletions
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py index 0a5758af..4117a0e5 100644 --- a/wqflask/wqflask/marker_regression/rqtl_mapping.py +++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py @@ -94,9 +94,6 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec ro.r('all_covars <- cbind(marker_covars, trait_covars)') else: ro.r('all_covars <- marker_covars') - #logger.info("Saving"); - #ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")') - #logger.info("Saving Done"); covars = ro.r['all_covars'] #DEBUG to save the session object to file if pair_scan: @@ -159,7 +156,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers type <- getGenoCode(header, 'type') if(type == '4-way'){ - genocodes <- c('1','2','3','4') + genocodes <- NULL } else { genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes } @@ -174,7 +171,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur require(qtl) if(type == '4-way'){ cat('Loading in as 4-WAY\n') - cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross + cross = read.cross(file=out, 'csvr', genotypes=NULL, crosstype="4way") # Load the created cross file using R/qtl read.cross }else if(type == 'f2'){ cat('Loading in as F2\n') cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="f2") # Load the created cross file using R/qtl read.cross @@ -332,8 +329,6 @@ def add_cofactors(cross, this_dataset, covariates, samples): covar_name_string += '"' + col_name + '", ' else: covar_name_string += '"' + col_name + '"' - - logger.info("covar_name_string:" + covar_name_string) else: col_name = "covar_" + str(i) cross = add_phenotype(cross, covar_as_string, col_name) @@ -343,7 +338,6 @@ def add_cofactors(cross, this_dataset, covariates, samples): covar_name_string += '"' + col_name + '"' covar_name_string += ")" - logger.info("covar_name_string:" + covar_name_string); covars_ob = pull_var("trait_covars", cross, covar_name_string) return cross, covars_ob |