Experimental Data Parsers¶
clinicalParser.py¶
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parse_dataset
(projectId, configuration, dataDir, key='project')[source]¶ This function parses clinical data from subjects in the project Input: uri of the clinical data file. Format: Subjects as rows, clinical variables as columns Output: pandas DataFrame with the same input format but the clinical variables mapped to the right ontology (defined in config), i.e. type = -40 -> SNOMED CT
proteomicsParser.py¶
wesParser.py¶
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loadWESDataset
(uri, configuration)[source]¶ This function gets the molecular data from a Whole Exome Sequencing experiment. Input: uri of the processed file resulting from the WES analysis pipeline. The resulting Annovar annotated VCF file from Mutect (sampleID_mutect_annovar.vcf) Output: pandas DataFrame with the columns and filters defined in config.py