diff options
| -rw-r--r-- | wqflask/wqflask/auwerx/phewas_analysis.py | 18 |
1 files changed, 16 insertions, 2 deletions
diff --git a/wqflask/wqflask/auwerx/phewas_analysis.py b/wqflask/wqflask/auwerx/phewas_analysis.py index 399e056c..c69326ed 100644 --- a/wqflask/wqflask/auwerx/phewas_analysis.py +++ b/wqflask/wqflask/auwerx/phewas_analysis.py @@ -21,16 +21,30 @@ from base import trait as TRAIT from utility import helper_functions from utility.tools import locate -from rpy2.robjects.packages import importr -utils = importr("utils") +r_library = ro.r["library"] # Map the library function +r_options = ro.r["options"] # Map the options function class PheWAS(object): def __init__(self): print("Initialization of PheWAS") + r_library("auwerx") # Load the auwerx package - Should only be done once, since it is quite expensive + r_options(stringsAsFactors = False) + # Create the aligners + r_download_BXD_geno = ro.r["download.BXD.geno"] # Map the create.Pheno_aligner function + r_create_Pheno_aligner = ro.r["create.Pheno_aligner"] # Map the create.Pheno_aligner function + r_create_SNP_aligner = ro.r["create.SNP_aligner"] # Map the create.SNP_aligner function + r_calculate_all_pvalue_parallel = ro.r["calculate.all.pvalue.parallel"] # Map the calculate.all.pvalue.parallel function + r_PheWASManhattan = ro.r["PheWASManhattan"] # Map the PheWASManhattan function print("Initialization of PheWAS done !") def run_analysis(self, requestform): print("Starting PheWAS analysis on dataset") + bxdgeno = r_download_BXD_geno() + snpaligner = r_create_SNP_aligner(bxdgeno) + phenoaligner = r_create_Pheno_aligner() + allpvalues = r_calculate_all_pvalue_parallel() # This needs some magic to work I think + # trait chromosome and trait positions should come from the user input + r_PheWASManhattan(None, allpvalues, phenoaligner, snpaligner, None, trait_chr, trait_pos, trait_pos ) print("Initialization of PheWAS done !") def process_results(self, results): |