Python generate_mutation_permutation_heat示例

示例#1

文件： findThreshold.py 项目： Yeung678/hotnet

def get_deltas_for_mutations(args, infmat, index2gene, heat_params):    
    print "* Performing permuted mutation data delta selection..."
    heat_permutations = permutations.generate_mutation_permutation_heat(
                            heat_params["heat_fn"], heat_params["sample_file"],
                            heat_params["gene_file"], index2gene.values(), heat_params["snv_file"],
                            args.gene_length_file, args.bmr, args.bmr_file, heat_params["cna_file"],
                            args.gene_order_file, heat_params["cna_filter_threshold"],
                            heat_params["min_freq"], args.num_permutations, args.parallel)
    return get_deltas_from_heat_permutations(infmat, index2gene, heat_permutations, args.parallel)

示例#2

文件： findThreshold.py 项目： raphael-group/hotnet

def get_deltas_for_mutations(args, infmat, index2gene, heat_params):
    print "* Performing permuted mutation data delta selection..."
    heat_permutations = permutations.generate_mutation_permutation_heat(
        heat_params["heat_fn"],
        heat_params["sample_file"], heat_params["gene_file"],
        index2gene.values(), heat_params["snv_file"], args.gene_length_file,
        args.bmr, args.bmr_file, heat_params["cna_file"], args.gene_order_file,
        heat_params["cna_filter_threshold"], heat_params["min_freq"],
        args.num_permutations, args.parallel)
    return get_deltas_from_heat_permutations(infmat, index2gene,
                                             heat_permutations, args.parallel)

示例#3

文件： runHotNet.py 项目： Yeung678/hotnet

def mutation_permutation_significance(args, infmat, infmat_index, G, heat_params):
    print "* Performing permuted mutation data statistical significance..."
    
    heat_permutations = permutations.generate_mutation_permutation_heat(
                            heat_params["heat_fn"], heat_params["sample_file"],
                            heat_params["gene_file"], infmat_index.values(), heat_params["snv_file"],
                            args.gene_length_file, args.bmr, args.bmr_file, heat_params["cna_file"],
                            args.gene_order_file, heat_params["cna_filter_threshold"],
                            heat_params["min_freq"], args.num_permutations, args.parallel)

    return calculate_significance(args, infmat, infmat_index, G, heat_permutations)

示例#4

def mutation_permutation_significance(args, infmat, infmat_index, G,
                                      heat_params):
    print "* Performing permuted mutation data statistical significance..."

    heat_permutations = permutations.generate_mutation_permutation_heat(
        heat_params["heat_fn"],
        heat_params["sample_file"], heat_params["gene_file"],
        infmat_index.values(), heat_params["snv_file"], args.gene_length_file,
        args.bmr, args.bmr_file, heat_params["cna_file"], args.gene_order_file,
        heat_params["cna_filter_threshold"], heat_params["min_freq"],
        args.num_permutations, args.parallel)

    return calculate_significance(args, infmat, infmat_index, G,
                                  heat_permutations)