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authorzsloan2021-01-06 11:51:01 -0600
committerzsloan2021-01-06 11:51:01 -0600
commit7bcc5d1e8111d7c74299c7f017c4a0427f8b4830 (patch)
tree63ff05a15e1e5ac14f650c29e1d10d73725c8a4e /wqflask
parent834a8c167df3c4d08c144fc614402347256e9af7 (diff)
downloadgenenetwork2-7bcc5d1e8111d7c74299c7f017c4a0427f8b4830.tar.gz
Changes to the way R/qtl deals with 4-way crosses so it will work with new HET3-ITP genotypes
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py10
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