MiScan¶

MiScan.core module¶

MiScan.core.generate_report(inDir, outDir, y_pred_pat)¶

generate report for single sample, including Cancer Risk Prediction | Top Gene Mutation Sites

Parameters:	inDir – for historical reason, actually, it’s the path of MISCAN.norm.trainPred.txt and

‘MISCAN.pat.trainPred.txt’ in dependency_data :param outDir: output directory :param y_pred_pat: risk_to_be_patient from func prediction :return:

MiScan.core.miscan_main(outDir, inVcf, model_weight='')¶: website sanctuary analysis core callable func :param model_weight: path of model weights :param outDir: temp, final result dir :param inVcf:input vcf full absolute path :return:no return

MiScan.core.prediction(outDir, model_weight)¶

predict single sample breast cancer risk

Parameters:	outDir – output directory model_weight – the MiScan model weight file path
Returns:	(risk_to_be_patient, probability_to_be_normal)

MiScan.core.vcf_to_sparse(outDir, inFeaID, inFeaBed, inVcf, featureID)¶: convert the vcf to a feature matrix, matrix.mtx :param outDir: output directory :param inFeaID: 13885fea_exon_cut_100bp_2sample.txt in dependency_data :param inFeaBed: tcga_13885fea_exon_cut_100bp.bed in dependency_data :param inVcf: the input vcf file path :param featureID: featureID.bed in dependency_data :return:

MiScan.logging.get_logger(name)¶

generate child logger

Parameters:	name – the name of logger
Returns:	child_logger

MiScan.model.build_dense_model(input_dim=13885, lr=1e-06, dropout=0.25, acti='leakyrelu')¶