feat/bg-18 ACMG - Adding PP2 #195
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jecos
approved these changes
Sep 13, 2023
jecos
reviewed
Sep 13, 2023
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| val orphanetDF = orphanet.select("gene_symbol", "average_age_of_onset", "type_of_inheritance") | ||
| .withColumn("is_adult_onset", inColArray("average_age_of_onset", onsets)) | ||
| .filter(col("is_adult_onset") === false) | ||
| .withColumn("is_dominant", inColArray("type_of_inheritance", is_dominant_inheritance)) | ||
| .select( | ||
| col("gene_symbol").as("symbol"), | ||
| col("is_dominant")) | ||
| .distinct() | ||
|
|
||
| val freqDF = frequencies | ||
| .select( | ||
| col("chromosome"), | ||
| col("start"), | ||
| col("end"), | ||
| col("reference"), | ||
| col("alternate"), | ||
| explode(col("genes_symbol")).as("symbol"), | ||
| col("external_frequencies.gnomad_genomes_3_1_1.ac").as("gnomad_ac"), | ||
| col("external_frequencies.gnomad_genomes_3_1_1.hom").as("gnomad_hom")) |
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Maynbe we should prepare a table offline, and join on this instead of calculating this dataframe each time?
jecos
approved these changes
Sep 13, 2023
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